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+      
+        <li class="md-nav__item">
+  <a href="#mailing-list" title="Mailing list" class="md-nav__link">
+    Mailing list
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+</li>
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 </li>
       
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+    Mailing list
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+</li>
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+  <a href="#how-to-update" title="How to update" class="md-nav__link">
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+  
+</li>
+      
       
       
       
@@ -1018,7 +1060,7 @@
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-                  <a href="https://github.com/lukasz-migas/ORIGAMI/tree/master/site-source/changelog/v1.2.1.1-27-12-2018.md" title="Edit this page" class="md-icon md-content__icon">&#xE3C9;</a>
+                  <a href="https://github.com/lukasz-migas/ORIGAMI/tree/master/site-source/changelog/v1.2.1.4-9-1-2019.md" title="Edit this page" class="md-icon md-content__icon">&#xE3C9;</a>
                 
                 
                 <h1 id="what-changed-in-origamianalyse">What changed in ORIGAMI<sup>ANALYSE</sup><a class="headerlink" href="#what-changed-in-origamianalyse" title="Permanent link">&para;</a></h1>
@@ -1044,7 +1086,7 @@ <h2 id="annotations">Annotations<a class="headerlink" href="#annotations" title=
 <p><img alt="Fixed" src="img/fixed.png" /> annotation parameters (e.g. size, weight, rotation) will be respected when replotting from the Document Tree</p>
 <h2 id="interactive-panel">Interactive panel<a class="headerlink" href="#interactive-panel" title="Permanent link">&para;</a></h2>
 <p><img alt="Added" src="img/added.png" /> Made big progres in terms of copying/applying styles for plot elements. When you
-double-click on any element in the file list a new window will appear where you can individually adjust plot parameters. When you finished, you can right-click on that same (or any other) item in the list and select 'Copy style..'.  You can then select any other item in the list, right-click on it and select 'Apply style..'.</p>
+double-click on any element in the file list a new window will appear where you can individually adjust plot parameters. When you finished, you can right-click on that same (or any other) item in the list and select 'Copy style..'. You can then select any other item in the list, right-click on it and select 'Apply style..'.</p>
 <p><img alt="Added" src="img/added.png" /> certain plot types (v-bar, h-bar, scatter, waterfall, multi-line/overlay) will now support addition of annotations (and their widgets). Annotations can correspond to anything you wish to say about specific region of a dataset.</p>
 <p><img alt="Added" src="img/added.png" /> Scatter plots that are created from datasets loaded through text files with added metadata can be enhanced with weblinks/URLs. See the <a href="https://origami.lukasz-migas.com/interactive-examples/ccs-compendium.html">example</a> for more information.</p>
 <p><img alt="Fixed" src="img/fixed.png" /> fixed sorting in the list (especilaly when using the 'Show selected' option) Lists are sorted using 'natural sorting' from now on, meaning they should be more logically sorted.</p>
@@ -1063,7 +1105,7 @@ <h2 id="uvpd-processing">UVPD processing <img alt="⭐" class="emojione" src="ht
 <h2 id="tandem-ms-panel">Tandem MS panel<a class="headerlink" href="#tandem-ms-panel" title="Permanent link">&para;</a></h2>
 <p><img alt="Added" src="img/added.png" /> You can now load .mzML files (haven't figured out how to add .mzIdentML files to them yet...)</p>
 <p><img alt="Added" src="img/added.png" /> MS/MS files can now be exported in an interactive format (.html document). This feature is still in development and I imagine will not be stable until v1.2.2 at the earliest. At the moment, individual scans of MS/MS file (.mgf only) can be annotated (e.g. fragments can be generated) and added to the file. Scans that have been user-annotated can be subsequently exported. This will be properly showcased in a tutorial.</p>
-<p><img alt="Added" src="img/added.png" /> Added two new options in the <strong>Action menu</strong> which permit improved population of the table by either exlcuding scans with PTMs and excluding scans without identification. Clicking on either of these will automatically trigger re-population of the table based on the selected options.</p>
+<p><img alt="Added" src="img/added.png" /> Added two new options in the <strong>Action menu</strong> which permit improved population of the table by either excluding scans with PTMs and excluding scans without identification. Clicking on either of these will automatically trigger re-population of the table based on the selected options.</p>
 <p><img alt="Added" src="img/added.png" /> You can see what PTMs have been included in the scan by clicking on the <strong>Modifications list</strong></p>
 <p><img alt="Improved" src="img/improved.png" /> Scans that have multiple identification information will be separated into separae instances in the table (e.g. look at the column ID #)</p>
 <p><img alt="Improved" src="img/improved.png" /> Fragment generator can now handle PTMs (at least those that have kept the mass information)</p>
@@ -1071,10 +1113,30 @@ <h2 id="tandem-ms-panel">Tandem MS panel<a class="headerlink" href="#tandem-ms-p
 <p><img alt="Improved" src="img/improved.png" /> Improved the way butterfly plots are shown. A horizontal line will be drawn from now on (at y=0)</p>
 <p><img alt="Improved" src="img/improved.png" /> Added several new customisation parameters that permit better data visualisation. These are found under <strong>Action -&gt; Customise...</strong></p>
 <p><img alt="Fixed" src="img/fixed.png" /> When selecting frag-all option, appropriate checkboxes will be ticked from now on</p>
+<p><img alt="Fixed" src="img/fixed.png" /> Fixed fragment generator to stop overriding fragments with same name (e.g. y1+ was equal y_H2Ox11+...)</p>
 <h2 id="other-data-annotated-data">Other data -&gt; Annotated data<a class="headerlink" href="#other-data-annotated-data" title="Permanent link">&para;</a></h2>
 <p><img alt="Added" src="img/added.png" /> Added new keyword 'axis_url'/'axis_urls' to the data parser. These keywords can be used to provide web addresses which can be attached to the data (scatter points only for now). If valid URL address is provided, when you tap on a point you will be taken to a new tab in your browser which corresponds to the web address. This is only valid in the interactive plots</p>
 <p><img alt="Changed" src="img/changed.png" /> Changed the poorly selected name of 'Other data' to 'Annotated data'</p>
 <h2 id="figures">Figures<a class="headerlink" href="#figures" title="Permanent link">&para;</a></h2>
+<p>Updated MS/MS panel</p>
+<p><img alt="MSMS" src="img/v1.2.1.4-9-1-2019/interactive_customise_item.png" /></p>
+<p>MS/MS customisation window</p>
+<p><img alt="MSMS" src="img/v1.2.1.4-9-1-2019/msms_settings.png" /></p>
+<p>Annotated MS/MS mass spectrum with automatically generated arrows</p>
+<p><img alt="MSMS" src="img/v1.2.1.4-9-1-2019/annotated_spectrum.png" /></p>
+<p>Interactive data customisation window</p>
+<p><img alt="Interactive" src="img/v1.2.1.4-9-1-2019/interactive_customise_item.png" /></p>
+<p>Interactive copy style</p>
+<p><img alt="Interactive" src="img/v1.2.1.4-9-1-2019/interactive_copy_style.png" /></p>
+<h2 id="animation">Animation<a class="headerlink" href="#animation" title="Permanent link">&para;</a></h2>
+<p>Interactive adjustment of labels</p>
+<p><img alt="Interactive" src="img/v1.2.1.4-9-1-2019/interactive_label_movement.gif" /></p>
+<h2 id="mailing-list">Mailing list<a class="headerlink" href="#mailing-list" title="Permanent link">&para;</a></h2>
+<p>If you would like to be added to the ORIGAMI mailing list where you will be notified of new releases, please contact <a href="mailto:lukasz.migas@manchester.ac.uk">lukasz.migas@manchester.ac.uk</a> or visit <a href="https://origami.lukasz-migas.com/main/subscribe.html">ORIGAMI documentation website</a>.</p>
+<h2 id="how-to-update">How to update<a class="headerlink" href="#how-to-update" title="Permanent link">&para;</a></h2>
+<p>A lot has changed in this version so the only way to update is to download the package and unpack it somewhere else on your PC. I've tried really hard not to break too many things :)</p>
+<p>Many thanks,
+Lukasz</p>
                 
                   
                 
diff --git a/docs/index.html b/docs/index.html
index 88dae1cf..c6ec103c 100644
--- a/docs/index.html
+++ b/docs/index.html
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index bb6da059..1742b97a 100644
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index d31a6b77..c9a10afb 100644
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@@ -248,7 +248,7 @@
   
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-        <a href="../changelog/v1.2.1.1-27-12-2018.html" title="Changelog" class="md-tabs__link">
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index 9ebc4e95..b39a3708 100644
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-{"config":{"lang":["en"],"prebuild_index":false,"separator":"[\\s\\-]+"},"docs":[{"location":"index.html","text":"Home About ORIGAMI-ANALYSE is a data processing and visualisation software The analysis software, ORIGAMI-ANALYSE can aid analysis of MS and IM-MS results from multiple instrumental platforms, offering rich data extraction, data processing and visualisation environment. Data can be imported from text (.csv/.txt/.tab), tandem MS (.mgf/.mzML/.mzIdent) and raw files (Waters .raw). ORIGAMI-ANALYSE was developed to handle a large number of files simultaneously, providing comparative and interactive environment to visualise results from multiple resources, generate publication-quality figures and interpret the results in more depth. All the processed data can be also exported as an interactive .html document that can be visualised in a web-browser and shared with your colleagues, reviewers or editors, as well as included as an SI. Main features Import single or multiple files (requires Driftscope for Waters .raw) Batch data extraction, processing and exporting Easy analysis and visualisation of aIM/CIU/SID datasets Highly customisable graphical environment to make high-quality figures Built-in CCS calibration and DT-IMS analysis Added functionality via plugins (e.g. UniDec deconvolution) Export all possible figures in an interactive .html document Getting started See the installation guide for instructions on how to get started. Examples A number of example files have been provided to get started! Please see various user guides and the examples page for more information. Main window","title":"Home"},{"location":"index.html#home","text":"","title":"Home"},{"location":"index.html#about","text":"ORIGAMI-ANALYSE is a data processing and visualisation software The analysis software, ORIGAMI-ANALYSE can aid analysis of MS and IM-MS results from multiple instrumental platforms, offering rich data extraction, data processing and visualisation environment. Data can be imported from text (.csv/.txt/.tab), tandem MS (.mgf/.mzML/.mzIdent) and raw files (Waters .raw). ORIGAMI-ANALYSE was developed to handle a large number of files simultaneously, providing comparative and interactive environment to visualise results from multiple resources, generate publication-quality figures and interpret the results in more depth. All the processed data can be also exported as an interactive .html document that can be visualised in a web-browser and shared with your colleagues, reviewers or editors, as well as included as an SI.","title":"About"},{"location":"index.html#main-features","text":"Import single or multiple files (requires Driftscope for Waters .raw) Batch data extraction, processing and exporting Easy analysis and visualisation of aIM/CIU/SID datasets Highly customisable graphical environment to make high-quality figures Built-in CCS calibration and DT-IMS analysis Added functionality via plugins (e.g. UniDec deconvolution) Export all possible figures in an interactive .html document","title":"Main features"},{"location":"index.html#getting-started","text":"See the installation guide for instructions on how to get started.","title":"Getting started"},{"location":"index.html#examples","text":"A number of example files have been provided to get started! Please see various user guides and the examples page for more information.","title":"Examples"},{"location":"index.html#main-window","text":"","title":"Main window"},{"location":"changelog/v1.2.0.3-5-11-2018.html","text":"Changes made in v1.2.0.3 General The underlying codebase of ORIGAMI has been improved to make it more readable and more responsive Item font color will be automatically adjusted to ensure best contrast from the background color in various lists in the GUI Logging of events was temporarily disabled as it appears to be causing some issues. I haven't been able to figure out why it crashes the program (yet). Tandem MS :star Added support to load .mgf and .mzIdentML file formats to visualise tandem mass spectrometry results. Menu - Open open-source files... to load .mgf files. You can then annotate the tandem MS with peptide fragments. See Figure 1 for example. Interactive panel Started adding support for individual modification of parameters for interactive plots (double-clicking on an item in the list) Issue that prevent proper showing of toolbar has been removed Peaklist panel Added 'Extract automatically' check tool (Peaklist - Toolbar - Extract...) Added a lot of new shortcuts for easier plotting Text file panel Added 'Extract automatically' check tool (Peaklist - Toolbar - Extract...) Removed an issue that would incorrectly remove documents from the text file list Multiple MS files panel The average mass spectrum can be re-binned/re-processed based on new parameters (Process - Average mass spectra (current document)) Removed an issue that prevented typing-in numerical values in the 'variable' colument when using laptop keyboards. I have only ever encountered this issue once... Let me know if it still occurs! Document tree Double-clicking on the document header will now clear all plots and show the most basic plots for that document (e.g. MS, DT, RT, etc). You can also do this by Right-click - Refresh document. Significant improvements to the right-click menus (most notably for UniDec/Annotations) Plots panel Some images can now be rotated by 90 degrees (mainly 2D) Wheel-zoom in the X-dimensions has been improved (works like on maps now) Data extraction You can now extract mass spectra from the '2D' panel. Hold CTRL on your keyboard and drag the mouse in the plot area. Only works when standard plot is shown (e.g. Drift time (bins) vs Scans/Time) Extracted mass spectra extracted in the DT and RT windows will be now shown in an area beneath the extraction plot (for convenience) MS annotations Peaks can now be annotated with an arrow (also available when exporting in an interactive format) Selection of a peak in the MS window using the mouse (Annotating: On) will automatically try to determine the charge state based on the peaks isotopic distribution. You can change the error tolerance in Action - Customise other settings - Charge prediction value (default: 0.05). UniDec settings Plots can now be customised using settings editor. (Settings: UniDec - Customise plots...) You can switch between tabbed view where each plot is in a separate tab OR continuous view where all plots are available on the same page (Customise plots... - Panel view) Deconvolution is now done in a multi-threaded mode. Should stop program from hanging All deconvolution results will be now stored in a temporary_data folder (found in ORIGAMI directory). This should keep your HDDs a little bit tidier. All files will be deleted at the end of the session. MS comparison You can now assign your own label to the plot. You can now compare ALL available mass spectra and not just those that were hidden under 'Mass Spectra' tag. (This includes: Mass Spectra, Mass Spectrum, Mass Spectrum (processed)). To open comparison panel: Menu - View - Open MS comparison panel...) Peak detection Works in multi-threaded mode. Should stop program from hanging.","title":"v1.2.0.3 - 7/11/2018"},{"location":"changelog/v1.2.0.3-5-11-2018.html#changes-made-in-v1203","text":"","title":"Changes made in v1.2.0.3"},{"location":"changelog/v1.2.0.3-5-11-2018.html#general","text":"The underlying codebase of ORIGAMI has been improved to make it more readable and more responsive Item font color will be automatically adjusted to ensure best contrast from the background color in various lists in the GUI Logging of events was temporarily disabled as it appears to be causing some issues. I haven't been able to figure out why it crashes the program (yet).","title":"General"},{"location":"changelog/v1.2.0.3-5-11-2018.html#tandem-ms-star","text":"Added support to load .mgf and .mzIdentML file formats to visualise tandem mass spectrometry results. Menu - Open open-source files... to load .mgf files. You can then annotate the tandem MS with peptide fragments. 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Should stop program from hanging.","title":"Peak detection"},{"location":"changelog/v1.2.1.1-27-12-2018.html","text":"What changed in ORIGAMI ANALYSE Documentation Added online documentation Added several new videos to the YouTube playlist Document Tree Fixed typo: spectrun - spectrum (grr) When loading mzml/mgf files, the individual scans will no longer be shown in the document tree as it caused some major issues. If you would like to see the individual spectra, please double-click on the header 'Tandem Mass Spectra' Fixed a problem when trying to plot waterfall plot from the Document Tree menu When loading any data into the INTERACTIVE document, you will be asked whether data should be duplicated, merged or duplicated When plotting a waterfall plot, data will be checked to ensure its not too big (e.g. not too many rows). If the value is above the threshold (set to 500), you will be asked if you would like to continue Main window Added new menu: Plugins . This menu will hold all future mini-applications Umder the menu Plot settings I've added a couple new options that allow modification of plot extra plot parameters. The help pages (Help - Help pages - ...) have now been replaced with links to the new documentation (opens in the browser). Where no documentation exists yet, old pages will be shown. Also available online Annotations you can now also easily 'duplicate/multiply' annotations. Action - Multiply annotations... this will result in a copy of the selected annotation(s) with slight difference in the min-value (so they can be distinguished from its parent) Text annotations can now be added to other plots (scatter, v-bar, h-bar, waterfall, multi-line/overlay). To added annotations, find it in the Document Tree , right-click on it and you should be presented with option Show annotations panel... . Then you can simply follow the standard annotations protocol. See here for more information Annotations parameters can now be easily modified as they can be dragged on the plot. If an annotation is shown on your plot, you can simply drag it around in the plot area and once you let-go, new settings (e.g. position) will be updated in the ORIGAMI document. font size, weight and rotation will now be aplied when adding labels auto-label generator will now also create labels based purely on the charge state annotation parameters (e.g. size, weight, rotation) will be respected when replotting from the Document Tree Interactive panel Made big progres in terms of copying/applying styles for plot elements. When you double-click on any element in the file list a new window will appear where you can individually adjust plot parameters. When you finished, you can right-click on that same (or any other) item in the list and select 'Copy style..'. You can then select any other item in the list, right-click on it and select 'Apply style..'. certain plot types (v-bar, h-bar, scatter, waterfall, multi-line/overlay) will now support addition of annotations (and their widgets). Annotations can correspond to anything you wish to say about specific region of a dataset. Scatter plots that are created from datasets loaded through text files with added metadata can be enhanced with weblinks/URLs. See the example for more information. fixed sorting in the list (especilaly when using the 'Show selected' option) Lists are sorted using 'natural sorting' from now on, meaning they should be more logically sorted. fixed the show/hide table elements when you right-click on the table headers Colorbars: added loads of new settings users can control better behaviour when adding colorbars to plots removed tools/toolset from ORIGAMI - the new system of copy/apply style should work much better I've realised that using 'coffeescript' for widget exportation was a big mistake as it takes ~10x+ longer to compile that script than pure JavaScript. Adding widgets will be a lot faster from now on (a couple haven't been ported to JS yet). Plots Improved color handling in violin and waterfall plots. The line color (edge) and shade/fill-under can be independently controlled now. UVPD processing Added new plug that allows analysis and processing of UVPD datasets that were acquired with laser being constantly switched on/off. This is a user-specific plugin that will most likely have no use for anyone else apart from some Barran group members. To activate, click on the Menu - Plugins - UVPD processing window... . Tandem MS panel You can now load .mzML files (haven't figured out how to add .mzIdentML files to them yet...) MS/MS files can now be exported in an interactive format (.html document). This feature is still in development and I imagine will not be stable until v1.2.2 at the earliest. At the moment, individual scans of MS/MS file (.mgf only) can be annotated (e.g. fragments can be generated) and added to the file. Scans that have been user-annotated can be subsequently exported. This will be properly showcased in a tutorial. Added two new options in the Action menu which permit improved population of the table by either exlcuding scans with PTMs and excluding scans without identification. Clicking on either of these will automatically trigger re-population of the table based on the selected options. You can see what PTMs have been included in the scan by clicking on the Modifications list Scans that have multiple identification information will be separated into separae instances in the table (e.g. look at the column ID #) Fragment generator can now handle PTMs (at least those that have kept the mass information) Improved the way scans are loaded (faster and actually works...) Improved the way butterfly plots are shown. A horizontal line will be drawn from now on (at y=0) Added several new customisation parameters that permit better data visualisation. These are found under Action - Customise... When selecting frag-all option, appropriate checkboxes will be ticked from now on Other data - Annotated data Added new keyword 'axis_url'/'axis_urls' to the data parser. These keywords can be used to provide web addresses which can be attached to the data (scatter points only for now). If valid URL address is provided, when you tap on a point you will be taken to a new tab in your browser which corresponds to the web address. This is only valid in the interactive plots Changed the poorly selected name of 'Other data' to 'Annotated data' Figures","title":"v1.2.1.1 - 27/12/2018"},{"location":"changelog/v1.2.1.1-27-12-2018.html#what-changed-in-origamianalyse","text":"","title":"What changed in ORIGAMIANALYSE"},{"location":"changelog/v1.2.1.1-27-12-2018.html#documentation","text":"Added online documentation Added several new videos to the YouTube playlist","title":"Documentation"},{"location":"changelog/v1.2.1.1-27-12-2018.html#document-tree","text":"Fixed typo: spectrun - spectrum (grr) When loading mzml/mgf files, the individual scans will no longer be shown in the document tree as it caused some major issues. If you would like to see the individual spectra, please double-click on the header 'Tandem Mass Spectra' Fixed a problem when trying to plot waterfall plot from the Document Tree menu When loading any data into the INTERACTIVE document, you will be asked whether data should be duplicated, merged or duplicated When plotting a waterfall plot, data will be checked to ensure its not too big (e.g. not too many rows). If the value is above the threshold (set to 500), you will be asked if you would like to continue","title":"Document Tree"},{"location":"changelog/v1.2.1.1-27-12-2018.html#main-window","text":"Added new menu: Plugins . This menu will hold all future mini-applications Umder the menu Plot settings I've added a couple new options that allow modification of plot extra plot parameters. The help pages (Help - Help pages - ...) have now been replaced with links to the new documentation (opens in the browser). Where no documentation exists yet, old pages will be shown. Also available online","title":"Main window"},{"location":"changelog/v1.2.1.1-27-12-2018.html#annotations","text":"you can now also easily 'duplicate/multiply' annotations. Action - Multiply annotations... this will result in a copy of the selected annotation(s) with slight difference in the min-value (so they can be distinguished from its parent) Text annotations can now be added to other plots (scatter, v-bar, h-bar, waterfall, multi-line/overlay). To added annotations, find it in the Document Tree , right-click on it and you should be presented with option Show annotations panel... . Then you can simply follow the standard annotations protocol. See here for more information Annotations parameters can now be easily modified as they can be dragged on the plot. If an annotation is shown on your plot, you can simply drag it around in the plot area and once you let-go, new settings (e.g. position) will be updated in the ORIGAMI document. font size, weight and rotation will now be aplied when adding labels auto-label generator will now also create labels based purely on the charge state annotation parameters (e.g. size, weight, rotation) will be respected when replotting from the Document Tree","title":"Annotations"},{"location":"changelog/v1.2.1.1-27-12-2018.html#interactive-panel","text":"Made big progres in terms of copying/applying styles for plot elements. When you double-click on any element in the file list a new window will appear where you can individually adjust plot parameters. When you finished, you can right-click on that same (or any other) item in the list and select 'Copy style..'. You can then select any other item in the list, right-click on it and select 'Apply style..'. certain plot types (v-bar, h-bar, scatter, waterfall, multi-line/overlay) will now support addition of annotations (and their widgets). Annotations can correspond to anything you wish to say about specific region of a dataset. Scatter plots that are created from datasets loaded through text files with added metadata can be enhanced with weblinks/URLs. See the example for more information. fixed sorting in the list (especilaly when using the 'Show selected' option) Lists are sorted using 'natural sorting' from now on, meaning they should be more logically sorted. fixed the show/hide table elements when you right-click on the table headers Colorbars: added loads of new settings users can control better behaviour when adding colorbars to plots removed tools/toolset from ORIGAMI - the new system of copy/apply style should work much better I've realised that using 'coffeescript' for widget exportation was a big mistake as it takes ~10x+ longer to compile that script than pure JavaScript. Adding widgets will be a lot faster from now on (a couple haven't been ported to JS yet).","title":"Interactive panel"},{"location":"changelog/v1.2.1.1-27-12-2018.html#plots","text":"Improved color handling in violin and waterfall plots. The line color (edge) and shade/fill-under can be independently controlled now.","title":"Plots"},{"location":"changelog/v1.2.1.1-27-12-2018.html#uvpd-processing","text":"Added new plug that allows analysis and processing of UVPD datasets that were acquired with laser being constantly switched on/off. This is a user-specific plugin that will most likely have no use for anyone else apart from some Barran group members. To activate, click on the Menu - Plugins - UVPD processing window... .","title":"UVPD processing"},{"location":"changelog/v1.2.1.1-27-12-2018.html#tandem-ms-panel","text":"You can now load .mzML files (haven't figured out how to add .mzIdentML files to them yet...) MS/MS files can now be exported in an interactive format (.html document). This feature is still in development and I imagine will not be stable until v1.2.2 at the earliest. At the moment, individual scans of MS/MS file (.mgf only) can be annotated (e.g. fragments can be generated) and added to the file. Scans that have been user-annotated can be subsequently exported. This will be properly showcased in a tutorial. Added two new options in the Action menu which permit improved population of the table by either exlcuding scans with PTMs and excluding scans without identification. Clicking on either of these will automatically trigger re-population of the table based on the selected options. You can see what PTMs have been included in the scan by clicking on the Modifications list Scans that have multiple identification information will be separated into separae instances in the table (e.g. look at the column ID #) Fragment generator can now handle PTMs (at least those that have kept the mass information) Improved the way scans are loaded (faster and actually works...) Improved the way butterfly plots are shown. A horizontal line will be drawn from now on (at y=0) Added several new customisation parameters that permit better data visualisation. These are found under Action - Customise... When selecting frag-all option, appropriate checkboxes will be ticked from now on","title":"Tandem MS panel"},{"location":"changelog/v1.2.1.1-27-12-2018.html#other-data-annotated-data","text":"Added new keyword 'axis_url'/'axis_urls' to the data parser. These keywords can be used to provide web addresses which can be attached to the data (scatter points only for now). If valid URL address is provided, when you tap on a point you will be taken to a new tab in your browser which corresponds to the web address. This is only valid in the interactive plots Changed the poorly selected name of 'Other data' to 'Annotated data'","title":"Other data -&gt; Annotated data"},{"location":"changelog/v1.2.1.1-27-12-2018.html#figures","text":"","title":"Figures"},{"location":"interactive-examples/ccs-compendium.html","text":"Interactive scatter plot Some background I recently came across this nice paper from John McLean's lab at Vanderbilt which discusses how we can use a relatively large (~4000 values) database of measured standards in omics studies. They have created a R Shiny app which provides interactivity to explore the dataset. Since I have been recently improving ORIGAMI's interactive capabilities, I've decided to embed their dataset in ORIGAMI and export it as a self-sufficient HTML document. This took me about ~10 minutes altogether (mostly rearranging columns and annotating text document). I think the results are quite close to the original publication (Figure 2a). See figure in another tab Interactive figure Formatted data You can have a look at the way the data is structured below. Download formatted data You can download the data used for this figure from here .","title":"CCS compendium"},{"location":"interactive-examples/ccs-compendium.html#interactive-scatter-plot","text":"","title":"Interactive scatter plot"},{"location":"interactive-examples/ccs-compendium.html#some-background","text":"I recently came across this nice paper from John McLean's lab at Vanderbilt which discusses how we can use a relatively large (~4000 values) database of measured standards in omics studies. They have created a R Shiny app which provides interactivity to explore the dataset. Since I have been recently improving ORIGAMI's interactive capabilities, I've decided to embed their dataset in ORIGAMI and export it as a self-sufficient HTML document. This took me about ~10 minutes altogether (mostly rearranging columns and annotating text document). I think the results are quite close to the original publication (Figure 2a). See figure in another tab","title":"Some background"},{"location":"interactive-examples/ccs-compendium.html#interactive-figure","text":"","title":"Interactive figure"},{"location":"interactive-examples/ccs-compendium.html#formatted-data","text":"You can have a look at the way the data is structured below.","title":"Formatted data"},{"location":"interactive-examples/ccs-compendium.html#download-formatted-data","text":"You can download the data used for this figure from here .","title":"Download formatted data"},{"location":"interactive-examples/heatmap.html","text":"Interactive heatmap Figures without widgets You can easily export heatmaps and share them with the scientific world! See figure in another tab Figure with widgets You can also annotate figure with multiple widgets that can improve the visualisation experience. It might be desirable to give readers/consumers the possibility to adjust the figure to their preferences. The example below shows how the colormap of the figure can be adjusted to bee more colorblind friendly and the reader can change the colormap too. See figure in another tab","title":"Heatmap"},{"location":"interactive-examples/heatmap.html#interactive-heatmap","text":"","title":"Interactive heatmap"},{"location":"interactive-examples/heatmap.html#figures-without-widgets","text":"You can easily export heatmaps and share them with the scientific world! See figure in another tab","title":"Figures without widgets"},{"location":"interactive-examples/heatmap.html#figure-with-widgets","text":"You can also annotate figure with multiple widgets that can improve the visualisation experience. It might be desirable to give readers/consumers the possibility to adjust the figure to their preferences. The example below shows how the colormap of the figure can be adjusted to bee more colorblind friendly and the reader can change the colormap too. See figure in another tab","title":"Figure with widgets"},{"location":"interactive-examples/mass-spectrum.html","text":"Interactive mass spectrum Figures without widgets You can easily export annotated mass spectrum and share it with the scientific world! Here is an example of a mass spectrum of a NIST antibody that you can zoom-in, move around, hover-over and more. See figure in another tab Figure with widgets You can also annotate figure with multiple widgets that can improve the visualisation experience. It might be desirable to give readers/consumers the possibility to adjust the figure to their preferences. The example below shows how labels can be removed, their size can be adjusted and the behaviour of the hover tool can be altered. See figure in another tab","title":"Mass spectrum"},{"location":"interactive-examples/mass-spectrum.html#interactive-mass-spectrum","text":"","title":"Interactive mass spectrum"},{"location":"interactive-examples/mass-spectrum.html#figures-without-widgets","text":"You can easily export annotated mass spectrum and share it with the scientific world! Here is an example of a mass spectrum of a NIST antibody that you can zoom-in, move around, hover-over and more. See figure in another tab","title":"Figures without widgets"},{"location":"interactive-examples/mass-spectrum.html#figure-with-widgets","text":"You can also annotate figure with multiple widgets that can improve the visualisation experience. It might be desirable to give readers/consumers the possibility to adjust the figure to their preferences. The example below shows how labels can be removed, their size can be adjusted and the behaviour of the hover tool can be altered. See figure in another tab","title":"Figure with widgets"},{"location":"interactive-examples/protemics-scans.html","text":"Interactive MS/MS spectra Some background Somewhat inspired by xiSPEC to bring proteomics data to the webbrowser, I've slowly been adding functionality to load and annotate MS/MS data. ORIGAMI can currently read .mgf and .mzml files as well as .mzid files. The mzIdentML files can be used as source of annotations (results) of the .mgf files (NOT .mzml...). When you load load a .mgf file, it will typically include 100s to 1000s of scans, each of which will contain 10s to 100s of peaks. The .mgf file does not store any annotation information (apart from precursor m/z, charge and a couple of other software specific annotations) so it must be supplemented with a .mzid file. In the example that I've used, the .mgf file contains ~4000 scans and when the .mzid file is loaded, each is annotated with appropriate peptide information and associated post-translational modification information. I have randomly selected a couple of scans and annotated them using the built-in fragment predictor (based on user-defined parameters) and as you can see below, when you select a scan, each 'dataset' includes data about the precursor (charge, peptide sequence, start/end position) and protein (including accession ID and protein sequence). In the current implementation, PTM information is not displayed below the plot, however is considered when generating fragments. Actions: Dropdown menu: Select dataset you are interested in Drag: Zoom-in on any plot area Hover: Discover information about peak including m/z, intensity, charge, fragment label, error, peptide sequence, modification See figure in another tab Interactive figure","title":"Proteomics - MS/MS"},{"location":"interactive-examples/protemics-scans.html#interactive-msms-spectra","text":"","title":"Interactive MS/MS spectra"},{"location":"interactive-examples/protemics-scans.html#some-background","text":"Somewhat inspired by xiSPEC to bring proteomics data to the webbrowser, I've slowly been adding functionality to load and annotate MS/MS data. ORIGAMI can currently read .mgf and .mzml files as well as .mzid files. The mzIdentML files can be used as source of annotations (results) of the .mgf files (NOT .mzml...). When you load load a .mgf file, it will typically include 100s to 1000s of scans, each of which will contain 10s to 100s of peaks. The .mgf file does not store any annotation information (apart from precursor m/z, charge and a couple of other software specific annotations) so it must be supplemented with a .mzid file. In the example that I've used, the .mgf file contains ~4000 scans and when the .mzid file is loaded, each is annotated with appropriate peptide information and associated post-translational modification information. I have randomly selected a couple of scans and annotated them using the built-in fragment predictor (based on user-defined parameters) and as you can see below, when you select a scan, each 'dataset' includes data about the precursor (charge, peptide sequence, start/end position) and protein (including accession ID and protein sequence). In the current implementation, PTM information is not displayed below the plot, however is considered when generating fragments. Actions: Dropdown menu: Select dataset you are interested in Drag: Zoom-in on any plot area Hover: Discover information about peak including m/z, intensity, charge, fragment label, error, peptide sequence, modification See figure in another tab","title":"Some background"},{"location":"interactive-examples/protemics-scans.html#interactive-figure","text":"","title":"Interactive figure"},{"location":"main/about.html","text":"About Author Lukasz G. Migas | Website | GitHub Getting in touch If you have any questions, encounter problems or would like to chat, please contact Lukasz Migas (lukasz.migas@manchester.ac.uk or lukas.migas@yahoo.com or @munieq11 ). Contributors Prof. Perdita E. Barran Bruno Bellina Aidan France Florian Benoit","title":"About"},{"location":"main/about.html#about","text":"","title":"About"},{"location":"main/about.html#author","text":"Lukasz G. Migas | Website | GitHub","title":"Author"},{"location":"main/about.html#getting-in-touch","text":"If you have any questions, encounter problems or would like to chat, please contact Lukasz Migas (lukasz.migas@manchester.ac.uk or lukas.migas@yahoo.com or @munieq11 ).","title":"Getting in touch"},{"location":"main/about.html#contributors","text":"Prof. Perdita E. Barran Bruno Bellina Aidan France Florian Benoit","title":"Contributors"},{"location":"main/bugs.html","text":"Report Bugs Go to the Google Forms If you've encountered any issues, please use this form to report them.","title":"Report Bugs"},{"location":"main/bugs.html#report-bugs","text":"","title":"Report Bugs"},{"location":"main/bugs.html#go-to-the-google-forms","text":"If you've encountered any issues, please use this form to report them.","title":"Go to the Google Forms"},{"location":"main/cite.html","text":"Citation Reference If you use ORIGAMI, please consider citing it in your work: L. G. Migas, A. P. France, B. Bellina, P. E. Barran, \"ORIGAMI: A software suite for activated ion mobility mass spectrometry (aIM-MS) applied to multimeric protein assemblies\u201d, Int. J. Mass Spectrom., 2017 RIS TY - JOUR T1 - ORIGAMI: A software suite for activated ion mobility mass spectrometry (aIM-MS) applied to multimeric protein assemblies AU - Migas, Lukasz G. AU - France, Aidan P. AU - Bellina, Bruno AU - Barran, Perdita E. JO - International Journal of Mass Spectrometry VL - 427 SP - 20 EP - 28 PY - 2018 DA - 2018/04/01/ T2 - Richard Smith Honor Issue SN - 1387-3806 DO - https://doi.org/10.1016/j.ijms.2017.08.014 UR - http://www.sciencedirect.com/science/article/pii/S1387380617302695 KW - Collision induced dissociation (CID) KW - Collision induced unfolding (CIU) KW - Activated ion mobility (aIM) KW - Ion mobility (IM) KW - Mass spectrometry (MS) KW - Software KW - Python AB - ER - BibTex @article{MIGAS201820, title = ORIGAMI: A software suite for activated ion mobility mass spectrometry (aIM-MS) applied to multimeric protein assemblies , journal = International Journal of Mass Spectrometry , volume = 427 , pages = 20 - 28 , year = 2018 , note = Richard Smith Honor Issue , issn = 1387-3806 , doi = https://doi.org/10.1016/j.ijms.2017.08.014 , url = http://www.sciencedirect.com/science/article/pii/S1387380617302695 , author = Lukasz G. Migas and Aidan P. France and Bruno Bellina and Perdita E. Barran , keywords = Collision induced dissociation (CID), Collision induced unfolding (CIU), Activated ion mobility (aIM), Ion mobility (IM), Mass spectrometry (MS), Software, Python }","title":"Cite"},{"location":"main/cite.html#citation","text":"","title":"Citation"},{"location":"main/cite.html#reference","text":"If you use ORIGAMI, please consider citing it in your work: L. G. Migas, A. P. France, B. Bellina, P. E. Barran, \"ORIGAMI: A software suite for activated ion mobility mass spectrometry (aIM-MS) applied to multimeric protein assemblies\u201d, Int. J. Mass Spectrom., 2017","title":"Reference"},{"location":"main/cite.html#ris","text":"TY - JOUR T1 - ORIGAMI: A software suite for activated ion mobility mass spectrometry (aIM-MS) applied to multimeric protein assemblies AU - Migas, Lukasz G. AU - France, Aidan P. AU - Bellina, Bruno AU - Barran, Perdita E. JO - International Journal of Mass Spectrometry VL - 427 SP - 20 EP - 28 PY - 2018 DA - 2018/04/01/ T2 - Richard Smith Honor Issue SN - 1387-3806 DO - https://doi.org/10.1016/j.ijms.2017.08.014 UR - http://www.sciencedirect.com/science/article/pii/S1387380617302695 KW - Collision induced dissociation (CID) KW - Collision induced unfolding (CIU) KW - Activated ion mobility (aIM) KW - Ion mobility (IM) KW - Mass spectrometry (MS) KW - Software KW - Python AB - ER -","title":"RIS"},{"location":"main/cite.html#bibtex","text":"@article{MIGAS201820, title = ORIGAMI: A software suite for activated ion mobility mass spectrometry (aIM-MS) applied to multimeric protein assemblies , journal = International Journal of Mass Spectrometry , volume = 427 , pages = 20 - 28 , year = 2018 , note = Richard Smith Honor Issue , issn = 1387-3806 , doi = https://doi.org/10.1016/j.ijms.2017.08.014 , url = http://www.sciencedirect.com/science/article/pii/S1387380617302695 , author = Lukasz G. Migas and Aidan P. France and Bruno Bellina and Perdita E. Barran , keywords = Collision induced dissociation (CID), Collision induced unfolding (CIU), Activated ion mobility (aIM), Ion mobility (IM), Mass spectrometry (MS), Software, Python }","title":"BibTex"},{"location":"main/installation.html","text":"Installation Download You can download the latest version of ORIGAMI-ANALYSE from GitHub . Getting Started Actually, there is no actual installation! Simply copy the zipped folder onto your machine, unpack it and that's it! To start ORIGAMI-ANALYSE, double-click on the ORIGAMI.exe file. Requirements Requirements: Windows 7/8/10 HDD space: ~1 Gb Optional: Waters Driftscope (v2.7+)","title":"Installation"},{"location":"main/installation.html#installation","text":"","title":"Installation"},{"location":"main/installation.html#download","text":"You can download the latest version of ORIGAMI-ANALYSE from GitHub .","title":"Download"},{"location":"main/installation.html#getting-started","text":"Actually, there is no actual installation! Simply copy the zipped folder onto your machine, unpack it and that's it! To start ORIGAMI-ANALYSE, double-click on the ORIGAMI.exe file.","title":"Getting Started"},{"location":"main/installation.html#requirements","text":"Requirements: Windows 7/8/10 HDD space: ~1 Gb Optional: Waters Driftscope (v2.7+)","title":"Requirements"},{"location":"main/request.html","text":"Request New Features Go to the Google Forms If you would like me to add new features to ORIGAMI-ANALYSE, please use this form to do so. Do it right here Loading...","title":"Request New Features"},{"location":"main/request.html#request-new-features","text":"","title":"Request New Features"},{"location":"main/request.html#go-to-the-google-forms","text":"If you would like me to add new features to ORIGAMI-ANALYSE, please use this form to do so.","title":"Go to the Google Forms"},{"location":"main/request.html#do-it-right-here","text":"Loading...","title":"Do it right here"},{"location":"main/subscribe.html","text":"#mc_embed_signup{background:#fff; clear:left; font:14px Helvetica,Arial,sans-serif; } /<em> Add your own Mailchimp form style overrides in your site stylesheet or in this style block. We recommend moving this block and the preceding CSS link to the HEAD of your HTML file. </em>/ Subscribe to our mailing list indicates required Email Address First Name Last Name","title":"Newsletter"},{"location":"user-guide/example-files.html","text":"Example files Please feel free to download any of the examples files to get started. Automated CIU - Waters (.raw) An example file that was used in the original publication and can be used as training in analysis of ORIGAMI MS file format. Download file Manual DT-IMS - Waters (.raw) A set of files acquired over a number of drift voltages on our ancient DT-IMS instrument Download file Mass spectrum - text An example mass spectrum to get an idea of the file format. Download file - IDP Download file - mAb Heatmap - text A collection of three processed heatmaps that were presented in the original publication. These can be loaded, visualised and compared against each other in ORIGAMI ANALYSE . Download file Other data with metadata - text A collection of example fils that permit addition of visualisation metadata that can be useful when exporting data in an interactive format. Download file","title":"Example files"},{"location":"user-guide/example-files.html#example-files","text":"Please feel free to download any of the examples files to get started.","title":"Example files"},{"location":"user-guide/example-files.html#automated-ciu-waters-raw","text":"An example file that was used in the original publication and can be used as training in analysis of ORIGAMI MS file format. Download file","title":"Automated CIU - Waters (.raw)"},{"location":"user-guide/example-files.html#manual-dt-ims-waters-raw","text":"A set of files acquired over a number of drift voltages on our ancient DT-IMS instrument Download file","title":"Manual DT-IMS - Waters (.raw)"},{"location":"user-guide/example-files.html#mass-spectrum-text","text":"An example mass spectrum to get an idea of the file format. Download file - IDP Download file - mAb","title":"Mass spectrum - text"},{"location":"user-guide/example-files.html#heatmap-text","text":"A collection of three processed heatmaps that were presented in the original publication. These can be loaded, visualised and compared against each other in ORIGAMI ANALYSE . Download file","title":"Heatmap - text"},{"location":"user-guide/example-files.html#other-data-with-metadata-text","text":"A collection of example fils that permit addition of visualisation metadata that can be useful when exporting data in an interactive format. Download file","title":"Other data with metadata - text"},{"location":"user-guide/loading-data.html","text":"Loading data How to load data There are several different ways how you can load your data Use the file menu. File - Open... Use the toolbar. Click on any of the available buttons Use a keyboard shortcut: CTRL+SHIFT+P - open ORIGAMI project file CTRL+R - open Waters (.raw) file - IM-MS CTRL+C - open Waters (.raw) file - CCS calibration CTRL+F - open Waters (.raw) file - DT-IMS CTRL+T - open heatmap text (.csv/.txt/.tab) file CTRL+SHIFT+C - open multiple heatmap text (.csv/.txt/.tab) files CTRL+V - get mass spectrum from clipboard Load directly from data panels (Multiple files, DT-IMS, Text files) Drag-and-drop files in the window or into the panel Supported file formats Raw files: Waters (.raw) MS and IM-MS Community files: Mascot Generic Format (.mgf), identification mzML (mzIdentML) Text: .csv/.txt/.tab - MS, DT, RT, heatmap, data with metadata Clipboard: - MS data only Supported datasets MS IM-MS CIU (manual and ORIGAMI MS acquired) SID (manual) UVPD IRMPD DT-IMS - still at experimental stage CCS calibration - still at experimental stage","title":"Opening files"},{"location":"user-guide/loading-data.html#loading-data","text":"","title":"Loading data"},{"location":"user-guide/loading-data.html#how-to-load-data","text":"There are several different ways how you can load your data Use the file menu. File - Open... Use the toolbar. Click on any of the available buttons Use a keyboard shortcut: CTRL+SHIFT+P - open ORIGAMI project file CTRL+R - open Waters (.raw) file - IM-MS CTRL+C - open Waters (.raw) file - CCS calibration CTRL+F - open Waters (.raw) file - DT-IMS CTRL+T - open heatmap text (.csv/.txt/.tab) file CTRL+SHIFT+C - open multiple heatmap text (.csv/.txt/.tab) files CTRL+V - get mass spectrum from clipboard Load directly from data panels (Multiple files, DT-IMS, Text files) Drag-and-drop files in the window or into the panel","title":"How to load data"},{"location":"user-guide/loading-data.html#supported-file-formats","text":"Raw files: Waters (.raw) MS and IM-MS Community files: Mascot Generic Format (.mgf), identification mzML (mzIdentML) Text: .csv/.txt/.tab - MS, DT, RT, heatmap, data with metadata Clipboard: - MS data only","title":"Supported file formats"},{"location":"user-guide/loading-data.html#supported-datasets","text":"MS IM-MS CIU (manual and ORIGAMI MS acquired) SID (manual) UVPD IRMPD DT-IMS - still at experimental stage CCS calibration - still at experimental stage","title":"Supported datasets"},{"location":"user-guide/data-handling/automated-ciu.html","text":"Analysis of ORIGAMI-MS datasets In this example we will use file provided with the ORIGAMI distribution. You can download it here or it should be found in your ORIGAMI directory ( example_data/origami_ms ). Data loading Please have a look at MS and IM-MS data loading . Data extraction Please have a look at MS and IM-MS data extraction . ORIGAMI-MS method ORIGAMI-MS acquired files are simply CIU datasets that were acquired within a single file in which the collision voltage (or cone voltage) were ramped to increase the activation energy. There are four methods available which either increase or keep constant the number of scans-per-voltage as the energy increases. Linear: the collision voltage (CV) is ramped from Start Voltage (StartV) to End Voltage (EndV) with Step Voltage (StepV) as the increment. The number of scans-per-voltage stays the same and is controlled by Scans per Voltage (SPV) . Exponential: the CV is ramped from StartV to EndV with StepV as the increment. The SPVs increase as a function of an exponential function where the user specifies the Exponential % and Exponential Increment . These values determine the rate of the increase. Boltzmann: the CV is ramped from StartV to EndV with StepV as the increment. The SPVs increase as a function of an Boltzmann function where the user specifies the Boltzmann Offset . These values determine the rate of the increase. User-defined: values of SPV and CV are provided in a list by the user. The user-defined list looks something like this and is usually provided as a .csv file. SPV CV 3 5 6 10 9 12 12 20 Getting started The first thing to consider when analysing ORIGAMI-MS based files is the fact that they have a definitive start and end. These two points correspond to the initial and final collision voltage used during the acquisition. ORIGAMI-MS inserts two reporter regions into the acquisition window, and they tend to manifest itself as significant (or sometimes not) dips in the signal intensity. If you started the acquisition correctly, they should be easy to spot. See below for an example How to determine first scan Change the view to the RT (chromatogram) tab Zoom-in on the 'reporter' region in the retention time plot. The first value after the break is the start scan which will be used later on. In this case, the start scan is 7 which means the first CV in the experiment was applied on the 7th scan. How to determine ORIGAMI-MS parameters There are only two ways you can determine what parameters were used in the acquisition. You saved them in your labbook or in the header of the MassLynx file (recommended) You saved them to a .csv file using the Save parameters button in ORIGAMI-MS window during your acquisition If you have done neither of these things, you can try to figure out your parameters by going to the folder containing ORIGAMI-MS program and looking for the appropriate ORIGAMI_log_ DATE-TIME .log file which contains all commands executed by the program. How to combine the same CVs into one This is a crucial step that will combine multiple scans into one, corresponding to the typical CIU file. First, you must select ions of interest in the MS and subsequently extract the data. Once you've done that, follow these steps. ORIGAMI-MS panel Open the Processing panel ( SHIFT+2 keyboard shortcut or Menu - Process - Settings: ORIGAMI or click on the button) Fill-in all necessary parameters (depending on your acquisition method). In the example case, we've used: start scan - 7 , start voltage - 4 , final voltage - 200 , step voltage - 2.0 , scans-per-voltage - 3 . Go to the Panel: Peaklist and select some or all extracted ions In the toolbar, click on the Process( ) button and select - Combine collision voltages for selected/all ions (ORIGAMI) Ions with combined CVs should appear in the Document tree under Drift time (2D, combined voltages, EIC) . The toolbar - Process menu: Comparison of the all-ion, extracted-ion and combined voltage EIC heatmaps: Extracting mass spectra for each CV Once you've associated ORIGAMI-MS parameters with the opened file, you can extract mass spectrum for each CV. Provide ORIGAMI-MS parameters (same as above #1) In the toolbar, click on the Process( ) button and select Extract mass spectra for each collision voltage (ORIGAMI). If the check Bin mass spectra during extraction is selected, mass spectra will be automatically linearized based on the parameters set in the Processing panel: Mass spectrum . Extraction can take several seconds - minutes. All MS data will appear in your document under Mass Spectra All extracted mass spectra shown in a waterfall-like plot Processing heatmaps By default, all heatmaps will show the raw data which might not always be the most visually pleasing. In some circumstances, it might be necessary to process (e.g. normalize or smooth) the data. Panel processing: 2D Select any number of ions in the peaklist. In the toolbar, click on the Process( ) button and select - Process selected/all ions. Ions will be process based on the parameters in the Processing panel: 2D . All process data will appear in the document with the (processed) tag attached to the name. Comparison of processing of some processing methods.","title":"Automated CIU datasets (ORIGAMI<sup>MS</sup>)"},{"location":"user-guide/data-handling/automated-ciu.html#analysis-of-origami-ms-datasets","text":"In this example we will use file provided with the ORIGAMI distribution. You can download it here or it should be found in your ORIGAMI directory ( example_data/origami_ms ).","title":"Analysis of ORIGAMI-MS datasets"},{"location":"user-guide/data-handling/automated-ciu.html#data-loading","text":"Please have a look at MS and IM-MS data loading .","title":"Data loading"},{"location":"user-guide/data-handling/automated-ciu.html#data-extraction","text":"Please have a look at MS and IM-MS data extraction .","title":"Data extraction"},{"location":"user-guide/data-handling/automated-ciu.html#origami-ms-method","text":"ORIGAMI-MS acquired files are simply CIU datasets that were acquired within a single file in which the collision voltage (or cone voltage) were ramped to increase the activation energy. There are four methods available which either increase or keep constant the number of scans-per-voltage as the energy increases. Linear: the collision voltage (CV) is ramped from Start Voltage (StartV) to End Voltage (EndV) with Step Voltage (StepV) as the increment. The number of scans-per-voltage stays the same and is controlled by Scans per Voltage (SPV) . Exponential: the CV is ramped from StartV to EndV with StepV as the increment. The SPVs increase as a function of an exponential function where the user specifies the Exponential % and Exponential Increment . These values determine the rate of the increase. Boltzmann: the CV is ramped from StartV to EndV with StepV as the increment. The SPVs increase as a function of an Boltzmann function where the user specifies the Boltzmann Offset . These values determine the rate of the increase. User-defined: values of SPV and CV are provided in a list by the user. The user-defined list looks something like this and is usually provided as a .csv file. SPV CV 3 5 6 10 9 12 12 20","title":"ORIGAMI-MS method"},{"location":"user-guide/data-handling/automated-ciu.html#getting-started","text":"The first thing to consider when analysing ORIGAMI-MS based files is the fact that they have a definitive start and end. These two points correspond to the initial and final collision voltage used during the acquisition. ORIGAMI-MS inserts two reporter regions into the acquisition window, and they tend to manifest itself as significant (or sometimes not) dips in the signal intensity. If you started the acquisition correctly, they should be easy to spot. See below for an example","title":"Getting started"},{"location":"user-guide/data-handling/automated-ciu.html#how-to-determine-first-scan","text":"Change the view to the RT (chromatogram) tab Zoom-in on the 'reporter' region in the retention time plot. The first value after the break is the start scan which will be used later on. In this case, the start scan is 7 which means the first CV in the experiment was applied on the 7th scan.","title":"How to determine first scan"},{"location":"user-guide/data-handling/automated-ciu.html#how-to-determine-origami-ms-parameters","text":"There are only two ways you can determine what parameters were used in the acquisition. You saved them in your labbook or in the header of the MassLynx file (recommended) You saved them to a .csv file using the Save parameters button in ORIGAMI-MS window during your acquisition If you have done neither of these things, you can try to figure out your parameters by going to the folder containing ORIGAMI-MS program and looking for the appropriate ORIGAMI_log_ DATE-TIME .log file which contains all commands executed by the program.","title":"How to determine ORIGAMI-MS parameters"},{"location":"user-guide/data-handling/automated-ciu.html#how-to-combine-the-same-cvs-into-one","text":"This is a crucial step that will combine multiple scans into one, corresponding to the typical CIU file. First, you must select ions of interest in the MS and subsequently extract the data. Once you've done that, follow these steps. ORIGAMI-MS panel Open the Processing panel ( SHIFT+2 keyboard shortcut or Menu - Process - Settings: ORIGAMI or click on the button) Fill-in all necessary parameters (depending on your acquisition method). In the example case, we've used: start scan - 7 , start voltage - 4 , final voltage - 200 , step voltage - 2.0 , scans-per-voltage - 3 . Go to the Panel: Peaklist and select some or all extracted ions In the toolbar, click on the Process( ) button and select - Combine collision voltages for selected/all ions (ORIGAMI) Ions with combined CVs should appear in the Document tree under Drift time (2D, combined voltages, EIC) . The toolbar - Process menu: Comparison of the all-ion, extracted-ion and combined voltage EIC heatmaps:","title":"How to combine the same CVs into one"},{"location":"user-guide/data-handling/automated-ciu.html#extracting-mass-spectra-for-each-cv","text":"Once you've associated ORIGAMI-MS parameters with the opened file, you can extract mass spectrum for each CV. Provide ORIGAMI-MS parameters (same as above #1) In the toolbar, click on the Process( ) button and select Extract mass spectra for each collision voltage (ORIGAMI). If the check Bin mass spectra during extraction is selected, mass spectra will be automatically linearized based on the parameters set in the Processing panel: Mass spectrum . Extraction can take several seconds - minutes. All MS data will appear in your document under Mass Spectra All extracted mass spectra shown in a waterfall-like plot","title":"Extracting mass spectra for each CV"},{"location":"user-guide/data-handling/automated-ciu.html#processing-heatmaps","text":"By default, all heatmaps will show the raw data which might not always be the most visually pleasing. In some circumstances, it might be necessary to process (e.g. normalize or smooth) the data. Panel processing: 2D Select any number of ions in the peaklist. In the toolbar, click on the Process( ) button and select - Process selected/all ions. Ions will be process based on the parameters in the Processing panel: 2D . All process data will appear in the document with the (processed) tag attached to the name. Comparison of processing of some processing methods.","title":"Processing heatmaps"},{"location":"user-guide/data-handling/manual-ciu.html","text":"Analysis of manual CIU/SID/multi-field DTIMS datasets In this example we will use files provided with the ORIGAMI distribution. You can download them here or it should be found in your ORIGAMI directory ( example_data/multi-field-dtims ). Manual CIU/SID/multi-field DTIMS Manual CIU/SID/DTIMS datasets consist of multiple files, each differing usually in the energy introduced to the system to either induce fragmentation or unfolding. In our case, we will be using CIU dataset where the collision energy was raised by several volts and we can observe some levels of unfolding. Data loading To load multiple Waters (.raw) files, please use any of the following: Use the file menu. File - Open multiple MassLynx (.raw) files [CIU] Use the toolbar. Click on the button Use a keyboard shortcut: CTRL+SHIFT-R - open multiple Waters (.raw) files - IM-MS Drag-and-drop files in the Multiple files panel When you have added files to ORIGAMI-ANALYSE, you will be asked to provide document name and document path. If you would like to add more files to the same document, make sure you click on the document in the Document tree and then use any of the above options to load data. Manual CIU document ORIGAMI-ANALYSE utilises documents to maintain all raw and processed data. The MANUAL document is a little different, as it requires different type of processing as it is pooling results from multiple files into one. When data is loaded, ORIGAMI-ANALYSE will only load the mass spectra and all-ion mobility data. In addition, a average mass spectrum will be generated from all spectra loaded in. This spectrum will be available under the Mass Spectrum tag in the document tree whereas individual spectra will be shown under the Mass Spectra sub-tree. Data extraction Although we are dealing with multiple files simulatenously now, data extraction is no different. Please have a look at MS and IM-MS data extraction . In short, you press-and-hold CTRL on your keyboard and drag with your mouse (while holding left-button) in the mass spectrum. An ion is added to the Panel: Peaklist from where you can extract its information. Stitching-up several files together When data is being extracted for specific ion, ORIGAMI-ANALYSE will use the 'variable' column in the Panel: Multiple files to determine the order in which files should be added. This column can be numerical (e.g. collision voltage, drift voltage) or alphabetical (e.g. name). If no value is provided, its not going to be pretty... Getting started The example provided is a set of files from a linear drift-tube experiment where each file corresponds to different drift voltage. So the variable that will be set in the table is the drift voltage and in this case, is written in the file name. When you have added these files to ORIGAMI-ANALYSE, you will be asked to specify document name and document path. In this case, yu can simply call it moqtof (name of the instrument it was acquired on). There are 6 files with drift voltages of 20, 25, 30, 35, 45, 50 and 60 V. As you will notice, when these files were added, the value of variable is set to 0, as the DV parameter is not saved in the MassLynx (.raw) file. You can specify by double-clicking in the variable column and typing appropriate value. Clicking on any column header will automatically sort the table. Panel: Multiple-files Combining data from multiple files into one Once you have added ions to the peaklist, you can extract that information . Changing x/y-axis labels By default, the label associated with combined dataset is 'Collision Voltage (V)' as it is expect to be a CIU-like dataset. In our case it is drift voltage, so once the ions have been combined, we can change the label in the Document Tree. Average mass spectrum The average mass spectrum generated when the data is being added to the document might not have the desired parameters. You can 're-average' the mass spectra by selecting relevant items int the filelist and then clicking on the Process... button and selecting Average mass spectra (current document) . ORIGAMI-ANALYSE will use the parameters set in the Processing panel: Mass Spectrum . Plotting and replotting The easiest way to plot anything in ORIGAMI-ANALYSE is to do it from the Document Tree and either double-clicking on the desired item or right-clicking and selecting appropriate option. Alternatively, you can right-click on an item in the Panel: Multiple-files and select either Show mass spectrum or Show mobiligram . Customising item Some parameters, such as variable or label can be changed by double-clicking in the appropriate field in the table and typing-in a value. Others, such as color can only be changed by right-clicking and selecint Assign new color . You also do this in batch by selecting several items in the list and clicking on the Annotate... button.","title":"Manual CIU/SID datasets"},{"location":"user-guide/data-handling/manual-ciu.html#analysis-of-manual-ciusidmulti-field-dtims-datasets","text":"In this example we will use files provided with the ORIGAMI distribution. You can download them here or it should be found in your ORIGAMI directory ( example_data/multi-field-dtims ).","title":"Analysis of manual CIU/SID/multi-field DTIMS datasets"},{"location":"user-guide/data-handling/manual-ciu.html#manual-ciusidmulti-field-dtims","text":"Manual CIU/SID/DTIMS datasets consist of multiple files, each differing usually in the energy introduced to the system to either induce fragmentation or unfolding. In our case, we will be using CIU dataset where the collision energy was raised by several volts and we can observe some levels of unfolding.","title":"Manual CIU/SID/multi-field DTIMS"},{"location":"user-guide/data-handling/manual-ciu.html#data-loading","text":"To load multiple Waters (.raw) files, please use any of the following: Use the file menu. File - Open multiple MassLynx (.raw) files [CIU] Use the toolbar. Click on the button Use a keyboard shortcut: CTRL+SHIFT-R - open multiple Waters (.raw) files - IM-MS Drag-and-drop files in the Multiple files panel When you have added files to ORIGAMI-ANALYSE, you will be asked to provide document name and document path. If you would like to add more files to the same document, make sure you click on the document in the Document tree and then use any of the above options to load data.","title":"Data loading"},{"location":"user-guide/data-handling/manual-ciu.html#manual-ciu-document","text":"ORIGAMI-ANALYSE utilises documents to maintain all raw and processed data. The MANUAL document is a little different, as it requires different type of processing as it is pooling results from multiple files into one. When data is loaded, ORIGAMI-ANALYSE will only load the mass spectra and all-ion mobility data. In addition, a average mass spectrum will be generated from all spectra loaded in. This spectrum will be available under the Mass Spectrum tag in the document tree whereas individual spectra will be shown under the Mass Spectra sub-tree.","title":"Manual CIU document"},{"location":"user-guide/data-handling/manual-ciu.html#data-extraction","text":"Although we are dealing with multiple files simulatenously now, data extraction is no different. Please have a look at MS and IM-MS data extraction . In short, you press-and-hold CTRL on your keyboard and drag with your mouse (while holding left-button) in the mass spectrum. An ion is added to the Panel: Peaklist from where you can extract its information.","title":"Data extraction"},{"location":"user-guide/data-handling/manual-ciu.html#stitching-up-several-files-together","text":"When data is being extracted for specific ion, ORIGAMI-ANALYSE will use the 'variable' column in the Panel: Multiple files to determine the order in which files should be added. This column can be numerical (e.g. collision voltage, drift voltage) or alphabetical (e.g. name). If no value is provided, its not going to be pretty...","title":"Stitching-up several files together"},{"location":"user-guide/data-handling/manual-ciu.html#getting-started","text":"The example provided is a set of files from a linear drift-tube experiment where each file corresponds to different drift voltage. So the variable that will be set in the table is the drift voltage and in this case, is written in the file name. When you have added these files to ORIGAMI-ANALYSE, you will be asked to specify document name and document path. In this case, yu can simply call it moqtof (name of the instrument it was acquired on). There are 6 files with drift voltages of 20, 25, 30, 35, 45, 50 and 60 V. As you will notice, when these files were added, the value of variable is set to 0, as the DV parameter is not saved in the MassLynx (.raw) file. You can specify by double-clicking in the variable column and typing appropriate value. Clicking on any column header will automatically sort the table. Panel: Multiple-files","title":"Getting started"},{"location":"user-guide/data-handling/manual-ciu.html#combining-data-from-multiple-files-into-one","text":"Once you have added ions to the peaklist, you can extract that information .","title":"Combining data from multiple files into one"},{"location":"user-guide/data-handling/manual-ciu.html#changing-xy-axis-labels","text":"By default, the label associated with combined dataset is 'Collision Voltage (V)' as it is expect to be a CIU-like dataset. In our case it is drift voltage, so once the ions have been combined, we can change the label in the Document Tree.","title":"Changing x/y-axis labels"},{"location":"user-guide/data-handling/manual-ciu.html#average-mass-spectrum","text":"The average mass spectrum generated when the data is being added to the document might not have the desired parameters. You can 're-average' the mass spectra by selecting relevant items int the filelist and then clicking on the Process... button and selecting Average mass spectra (current document) . ORIGAMI-ANALYSE will use the parameters set in the Processing panel: Mass Spectrum .","title":"Average mass spectrum"},{"location":"user-guide/data-handling/manual-ciu.html#plotting-and-replotting","text":"The easiest way to plot anything in ORIGAMI-ANALYSE is to do it from the Document Tree and either double-clicking on the desired item or right-clicking and selecting appropriate option. Alternatively, you can right-click on an item in the Panel: Multiple-files and select either Show mass spectrum or Show mobiligram .","title":"Plotting and replotting"},{"location":"user-guide/data-handling/manual-ciu.html#customising-item","text":"Some parameters, such as variable or label can be changed by double-clicking in the appropriate field in the table and typing-in a value. Others, such as color can only be changed by right-clicking and selecint Assign new color . You also do this in batch by selecting several items in the list and clicking on the Annotate... button.","title":"Customising item"},{"location":"user-guide/data-handling/ms-and-imms-files.html","text":"Analysis of MS and IM-MS files In this example, we will use a file provided in the example. You can download it from here or it should be found in your ORIGAMI directory ( example_data/origami_ms ). Video tutorial of how to load and process Waters (.raw) files Data loading To load Waters (.raw) files, please use any of the following: Use the file menu. File - Open ORIGAMI MassLynx (.raw) file [CIU] Use the toolbar. Click on the button Use a keyboard shortcut: CTRL+R - open Waters (.raw) file - IM-MS Drag-and-drop the file in the main window Document tree Any file you open will result in generation of a ORIGAMI document that will contain all data that you will generate. It is structured just like a directory on your PC so it should be easy to get used to. When you right-click on any item, a custom menu will appear from which you can figure out what you would like to do. An example is shown below: Plotting and replotting You can either double-click on an item in the Document tree or right-click and select the option \"Show...\". If you would like to clear a plot, right-click in the plot area and select \"Clear plot\". Data extraction You can extract various types of data from Waters (.raw) files. The type you extract will depend on the window you are currently viewing. So, if you are in the MS window, you can extract heatmap , mobility and chromatography data. If you are in the RT , 1D or 2D windows, you can extract mass spectra . To select region you would like to extract, press and hold CTRL on your keyboard and left-click drag your mouse on the selected region. Most data will be automatically extracted (except for heatmaps - will discuss shortly). Data that has been extracted will be automatically added to your document . Mass spectra (from RT, 1D, 2D windows) The extracted mass spectra can either represent the raw data or linearized data, depending on what settings you have enabled. To change this behaviour, open the Processing window , go to Mass spectrum and check (or uncheck) the \"Enable MS linearization in chromatogram/mobiligram window\". You can also change linearization settings in this panel. If you are extracting from the RT window, chromatographic information will be used, from the 1D window, drift time and from 2D window, both will be used. Extracted data will appear under Mass Spectra . Video tutorial of how to extract mass spectra from Waters (.raw) files Heatmaps (from MS window) When you extract data from the MS window, an ion will automatically be added to the Peaklist. This panel serves as main select-and-compare tool for easy visualisation of multiple items together. In order for the data to be extracted, you must click on the button and a new menu will appear where appear where you can select the \"Extract all ions\". If, in future you would like to automatically extract heatmaps, click on the \"Extract automatically\" toggle. Extracted data will appear under Drift time (2D, EIC) . Chromatograms (from DT/MS window) You can extract chromatograms in the DT/MS window where the m/z and drift time information will be taken into account during data extraction. Extracted data will appear under Chromatograms (EIC) . Panel: Peaklist All heatmaps are automatically added to the Panel peaklist which usually appears on the right-hand side of the window. From here, you can easily visualise, customise and compare data. When you right-click on any item in the list, a menu will appear from which you can easily access various visualisation modes and customisation settings. When you double-click on an item (or right-click and select \"Edit file information\") a new window will appear where you can change certain parameters, such as ORIGAMI MS parameters, charge state, color, colormap, etc . Processing mass spectra Mass spectra imported using Driftscope are automatically normalized to 1 (not my fault, I promise!). Sometimes, it might be necessary to remove noise or smooth the spectrum so it is more visually appealing. Panel processing: MS Right-click on any mass spectrum in the Document tree (e.g. Mass Spectrum) and select Process... . A new window will appear where you can adjust processing parameters. Click on the Replot button if you first want to see how the data will look or Process if you would like to add that data to the document. Processing heatmaps By default, all heatmaps will show the raw data which might not always be the most visually pleasing. In some circumstances, it might be necessary to process (e.g. normalize or smooth) the data. Panel processing: 2D Depending what are you planning on processing (e.g. extracted ion heatmap or whole-file heatmap), you can perform processing in the Panel: Peaklist or in the Document tree . Processing from Panel: Peaklist Select any number of ions in the peaklist. In the toolbar, click on the Process( ) button and select - Process selected/all ions. Ions will be process based on the parameters in the Processing panel: 2D . All process data will appear in the document with the (processed) tag attached to the name. Processing from Document tree Right-click on a desired item in the Document tree (e.g. Drift time (2D)) and select Process... A new window will appear where you can adjust processing parameters Click on the Replot button if you first want to see how the data will look or Process if you would like to add that data to the document. Comparison of processing of some of the processing methods","title":"MS and IM-MS files"},{"location":"user-guide/data-handling/ms-and-imms-files.html#analysis-of-ms-and-im-ms-files","text":"In this example, we will use a file provided in the example. You can download it from here or it should be found in your ORIGAMI directory ( example_data/origami_ms ).","title":"Analysis of MS and IM-MS files"},{"location":"user-guide/data-handling/ms-and-imms-files.html#video-tutorial-of-how-to-load-and-process-waters-raw-files","text":"","title":"Video tutorial of how to load and process Waters (.raw) files"},{"location":"user-guide/data-handling/ms-and-imms-files.html#data-loading","text":"To load Waters (.raw) files, please use any of the following: Use the file menu. File - Open ORIGAMI MassLynx (.raw) file [CIU] Use the toolbar. Click on the button Use a keyboard shortcut: CTRL+R - open Waters (.raw) file - IM-MS Drag-and-drop the file in the main window","title":"Data loading"},{"location":"user-guide/data-handling/ms-and-imms-files.html#document-tree","text":"Any file you open will result in generation of a ORIGAMI document that will contain all data that you will generate. It is structured just like a directory on your PC so it should be easy to get used to. When you right-click on any item, a custom menu will appear from which you can figure out what you would like to do. An example is shown below:","title":"Document tree"},{"location":"user-guide/data-handling/ms-and-imms-files.html#plotting-and-replotting","text":"You can either double-click on an item in the Document tree or right-click and select the option \"Show...\". If you would like to clear a plot, right-click in the plot area and select \"Clear plot\".","title":"Plotting and replotting"},{"location":"user-guide/data-handling/ms-and-imms-files.html#data-extraction","text":"You can extract various types of data from Waters (.raw) files. The type you extract will depend on the window you are currently viewing. So, if you are in the MS window, you can extract heatmap , mobility and chromatography data. If you are in the RT , 1D or 2D windows, you can extract mass spectra . To select region you would like to extract, press and hold CTRL on your keyboard and left-click drag your mouse on the selected region. Most data will be automatically extracted (except for heatmaps - will discuss shortly). Data that has been extracted will be automatically added to your document .","title":"Data extraction"},{"location":"user-guide/data-handling/ms-and-imms-files.html#mass-spectra-from-rt-1d-2d-windows","text":"The extracted mass spectra can either represent the raw data or linearized data, depending on what settings you have enabled. To change this behaviour, open the Processing window , go to Mass spectrum and check (or uncheck) the \"Enable MS linearization in chromatogram/mobiligram window\". You can also change linearization settings in this panel. If you are extracting from the RT window, chromatographic information will be used, from the 1D window, drift time and from 2D window, both will be used. Extracted data will appear under Mass Spectra .","title":"Mass spectra (from RT, 1D, 2D windows)"},{"location":"user-guide/data-handling/ms-and-imms-files.html#video-tutorial-of-how-to-extract-mass-spectra-from-waters-raw-files","text":"","title":"Video tutorial of how to extract mass spectra from Waters (.raw) files"},{"location":"user-guide/data-handling/ms-and-imms-files.html#heatmaps-from-ms-window","text":"When you extract data from the MS window, an ion will automatically be added to the Peaklist. This panel serves as main select-and-compare tool for easy visualisation of multiple items together. In order for the data to be extracted, you must click on the button and a new menu will appear where appear where you can select the \"Extract all ions\". If, in future you would like to automatically extract heatmaps, click on the \"Extract automatically\" toggle. Extracted data will appear under Drift time (2D, EIC) .","title":"Heatmaps (from MS window)"},{"location":"user-guide/data-handling/ms-and-imms-files.html#chromatograms-from-dtms-window","text":"You can extract chromatograms in the DT/MS window where the m/z and drift time information will be taken into account during data extraction. Extracted data will appear under Chromatograms (EIC) .","title":"Chromatograms (from DT/MS window)"},{"location":"user-guide/data-handling/ms-and-imms-files.html#panel-peaklist","text":"All heatmaps are automatically added to the Panel peaklist which usually appears on the right-hand side of the window. From here, you can easily visualise, customise and compare data. When you right-click on any item in the list, a menu will appear from which you can easily access various visualisation modes and customisation settings. When you double-click on an item (or right-click and select \"Edit file information\") a new window will appear where you can change certain parameters, such as ORIGAMI MS parameters, charge state, color, colormap, etc .","title":"Panel: Peaklist"},{"location":"user-guide/data-handling/ms-and-imms-files.html#processing-mass-spectra","text":"Mass spectra imported using Driftscope are automatically normalized to 1 (not my fault, I promise!). Sometimes, it might be necessary to remove noise or smooth the spectrum so it is more visually appealing.","title":"Processing mass spectra"},{"location":"user-guide/data-handling/ms-and-imms-files.html#panel-processing-ms","text":"Right-click on any mass spectrum in the Document tree (e.g. Mass Spectrum) and select Process... . A new window will appear where you can adjust processing parameters. Click on the Replot button if you first want to see how the data will look or Process if you would like to add that data to the document.","title":"Panel processing: MS"},{"location":"user-guide/data-handling/ms-and-imms-files.html#processing-heatmaps","text":"By default, all heatmaps will show the raw data which might not always be the most visually pleasing. In some circumstances, it might be necessary to process (e.g. normalize or smooth) the data.","title":"Processing heatmaps"},{"location":"user-guide/data-handling/ms-and-imms-files.html#panel-processing-2d","text":"Depending what are you planning on processing (e.g. extracted ion heatmap or whole-file heatmap), you can perform processing in the Panel: Peaklist or in the Document tree .","title":"Panel processing: 2D"},{"location":"user-guide/data-handling/ms-and-imms-files.html#processing-from-panel-peaklist","text":"Select any number of ions in the peaklist. In the toolbar, click on the Process( ) button and select - Process selected/all ions. Ions will be process based on the parameters in the Processing panel: 2D . All process data will appear in the document with the (processed) tag attached to the name.","title":"Processing from Panel: Peaklist"},{"location":"user-guide/data-handling/ms-and-imms-files.html#processing-from-document-tree","text":"Right-click on a desired item in the Document tree (e.g. Drift time (2D)) and select Process... A new window will appear where you can adjust processing parameters Click on the Replot button if you first want to see how the data will look or Process if you would like to add that data to the document.","title":"Processing from Document tree"},{"location":"user-guide/data-handling/ms-and-imms-files.html#comparison-of-processing-of-some-of-the-processing-methods","text":"","title":"Comparison of processing of some of the processing methods"},{"location":"user-guide/data-handling/text-files.html","text":"Analysis of text files In this example we will use files provided with the ORIGAMI distribution. You can download MS file and heatmap file or you can find them in your ORIGAMI directory ( example_data/text ). Data loading To load text files, please use any of the following: Use the file menu. File - Open IM-MS Text file [CIU] or Open MS Text file Use the toolbar. Click on the T or T+ button Use a keyboard shortcut: CTRL+T - open heatmap text (.csv/.txt/.tab) file Drag-and-drop the file in the main window Clipboard: - MS data only Document tree Any file you open will result in generation of a ORIGAMI document that will contain all data that you will generate. It is structured just like a directory on your PC so it should be easy to get used to. When you right-click on any item, a custom menu will appear from which you can figure out what you would like to do. An example is shown below: Plotting and replotting You can either double-click on an item in the Document tree or right-click and select the option \"Show...\". If you would like to clear a plot, right-click in the plot area and select \"Clear plot\". Panel: Textlist All text-based heatmaps are automatically added to the Panel textlist which usually appears on the right-hand side of the window. From here, you can easily visualise, customise and compare data. When you right-click on any item in the list, a menu will appear from which you can easily access various visualisation modes and customisation settings. When you double-click on an item (or right-click and select \"Edit file information\") a new window will appear where you can change certain parameters, such as charge state, color, colormap, etc . Processing heatmaps By default, all heatmaps will show the raw data which might not always be the most visually pleasing. In some circumstances, it might be necessary to process (e.g. normalize or smooth) the data. Processing panel: 2D Processing from Panel: Textlist Select any number of ions in the textlist. In the toolbar, click on the Process( ) button and select - Process selected/all ions. Ions will be process based on the parameters in the Processing panel: 2D . All process data will appear in the document with the (processed) tag attached to the name. Processing from Document tree Right-click on a desired item in the Document tree (e.g. Drift time (2D)) and select Process... A new window will appear where you can adjust processing parameters Click on the Replot button if you first want to see how the data will look or Process if you would like to add that data to the document.","title":"Text files"},{"location":"user-guide/data-handling/text-files.html#analysis-of-text-files","text":"In this example we will use files provided with the ORIGAMI distribution. You can download MS file and heatmap file or you can find them in your ORIGAMI directory ( example_data/text ).","title":"Analysis of text files"},{"location":"user-guide/data-handling/text-files.html#data-loading","text":"To load text files, please use any of the following: Use the file menu. File - Open IM-MS Text file [CIU] or Open MS Text file Use the toolbar. Click on the T or T+ button Use a keyboard shortcut: CTRL+T - open heatmap text (.csv/.txt/.tab) file Drag-and-drop the file in the main window Clipboard: - MS data only","title":"Data loading"},{"location":"user-guide/data-handling/text-files.html#document-tree","text":"Any file you open will result in generation of a ORIGAMI document that will contain all data that you will generate. It is structured just like a directory on your PC so it should be easy to get used to. When you right-click on any item, a custom menu will appear from which you can figure out what you would like to do. An example is shown below:","title":"Document tree"},{"location":"user-guide/data-handling/text-files.html#plotting-and-replotting","text":"You can either double-click on an item in the Document tree or right-click and select the option \"Show...\". If you would like to clear a plot, right-click in the plot area and select \"Clear plot\".","title":"Plotting and replotting"},{"location":"user-guide/data-handling/text-files.html#panel-textlist","text":"All text-based heatmaps are automatically added to the Panel textlist which usually appears on the right-hand side of the window. From here, you can easily visualise, customise and compare data. When you right-click on any item in the list, a menu will appear from which you can easily access various visualisation modes and customisation settings. When you double-click on an item (or right-click and select \"Edit file information\") a new window will appear where you can change certain parameters, such as charge state, color, colormap, etc .","title":"Panel: Textlist"},{"location":"user-guide/data-handling/text-files.html#processing-heatmaps","text":"By default, all heatmaps will show the raw data which might not always be the most visually pleasing. In some circumstances, it might be necessary to process (e.g. normalize or smooth) the data.","title":"Processing heatmaps"},{"location":"user-guide/data-handling/text-files.html#processing-panel-2d","text":"","title":"Processing panel: 2D"},{"location":"user-guide/data-handling/text-files.html#processing-from-panel-textlist","text":"Select any number of ions in the textlist. In the toolbar, click on the Process( ) button and select - Process selected/all ions. Ions will be process based on the parameters in the Processing panel: 2D . All process data will appear in the document with the (processed) tag attached to the name.","title":"Processing from Panel: Textlist"},{"location":"user-guide/data-handling/text-files.html#processing-from-document-tree","text":"Right-click on a desired item in the Document tree (e.g. Drift time (2D)) and select Process... A new window will appear where you can adjust processing parameters Click on the Replot button if you first want to see how the data will look or Process if you would like to add that data to the document.","title":"Processing from Document tree"},{"location":"user-guide/deconvolution/unidec-change-window-view.html","text":"Changing UniDec window Since version 1.2.0.3, ORIGAMI-ANALYSE shows UniDec plots in a seperate tab rather than in the continous view. It is quite straightforward to switch back to the continous view . Open the Processing panel: UniDec ( SHIFT+6 on your keyboard or menu - Process - UniDec). Click on the Customise plots... button Change the setting: Panel view to what you would prefer. Note: This will only take effect when you restart ORIGAMI-ANALYSE.","title":"UniDec - changing window view "},{"location":"user-guide/deconvolution/unidec-change-window-view.html#changing-unidec-window","text":"Since version 1.2.0.3, ORIGAMI-ANALYSE shows UniDec plots in a seperate tab rather than in the continous view. It is quite straightforward to switch back to the continous view . Open the Processing panel: UniDec ( SHIFT+6 on your keyboard or menu - Process - UniDec). Click on the Customise plots... button Change the setting: Panel view to what you would prefer. Note: This will only take effect when you restart ORIGAMI-ANALYSE.","title":"Changing UniDec window"},{"location":"user-guide/deconvolution/unidec-customise-plots.html","text":"Customising UniDec plots In the case of UniDec plots, several parameters such as color schemes , marker size , heatmap parameters and others can be adjusted by opening the Processing panel: UniDec and then the Customisation panel . Open the Processing panel: UniDec ( SHIFT+6 on your keyboard or menu - Process - UniDec). Click on the Customise plots... button As you can see, most parameters have been split based on which plot they are applied to. You can simply change the parameter value, close the window and then replot the plot you want to improve (settings are not applied automatically). Settings such as line widths, line styles, figure size or label size can be adjusted through the Plot Editor panel that is accessible through (Menu - Plot settings or the toolbar icons )","title":"UniDec - customising plots "},{"location":"user-guide/deconvolution/unidec-customise-plots.html#customising-unidec-plots","text":"In the case of UniDec plots, several parameters such as color schemes , marker size , heatmap parameters and others can be adjusted by opening the Processing panel: UniDec and then the Customisation panel . Open the Processing panel: UniDec ( SHIFT+6 on your keyboard or menu - Process - UniDec). Click on the Customise plots... button As you can see, most parameters have been split based on which plot they are applied to. You can simply change the parameter value, close the window and then replot the plot you want to improve (settings are not applied automatically). Settings such as line widths, line styles, figure size or label size can be adjusted through the Plot Editor panel that is accessible through (Menu - Plot settings or the toolbar icons )","title":"Customising UniDec plots"},{"location":"user-guide/deconvolution/unidec-deconvolution.html","text":"UniDec deconvolution UniDec is a Bayesian deconvolution algorithm that can be used to deconvolute mass spectra and ion mobility-mass spectra. It was developed by Dr. Michael Marty and is freely available under the modified BSD licence. I would highly recommend you check-out UniDec (and MetaUniDec) software. If you use it in your work, please cite their work: M. T. Marty, A. J. Baldwin, E. G. Marklund, G. K. A. Hochberg, J. L. P. Benesch, C. V. Robinson, Anal. Chem. 2015, 87, 4370-4376. Video tutorial Deconvolution in ORIGAMI-ANALYSE Any mass spectrum within a ORIGAMI document can be deconvoluted and therefore a document can contain tens of spectra, each with its own deconvolution results. The easiest way to get started is to find an item in the Document Tree, right-click on it and select Deconvolute using UniDec... which will open a new panel where you can adjust the parameters. Example data In this example we will use a file provided with the ORIGAMI distribution. You can download MS file or you can find it in your ORIGAMI directory ( example_data/text ). This file contains a mass spectrum of a intrinsically disordered protein, p27 that is approx. 22.5 kDa in size and has a very broad charge state distribution. Loading data Please have a look at Loading Text files . In short, you either drag-and-drop the text file in the main window of ORIGAMI-ANALYSE or go to File - Open MS Text file . Deconvolution Once you've loaded data, right-click on it in the Document Tree and select Deconvolute using UniDec... If you are using the example file, you can start with the settings shown below: Specify Pre-processing parameters. You can start with m/z start = 500 and m/z end = 2500 with m/z bin size = 0.1 using Linear interpolation method. Click on the Pre-process button. If you are using the Tabbed view , the results will be shown in the tab UniDec - MS Specify deconvolution parameters. If you are unsure about the sample you are analysing, specify a broad range of charge states and the molecular weight with large-ish Sampling frequency. This will help you narrow down the appropriate range for your sample. Once you are happy, click on the Run UniDec button. If you are using the Tabbed view , the results will be shown in UniDec - m/z vs Charge / MW vs Charge / MW tabs. Following successful deconvolution, you can find peaks and identify the found molecular weights. To do this, specify appropriate parameters in the Peak detection parameters section and then click on the Detect peaks button. If you are using the Tabbed view , the results will be shown in UniDec - Isolated MS / Barplot tabs. Visualisation of results Visualisation of individual species If you are lucky, deconvolution will result in a single species being detect. This is rather unlikely and therefore you will be presented with a range of detected MW. In order to select and visualise only one species at at time, you can select an item with a molecular weight in the Dropdown menu (see below) and click on the Isolate button. You can also label its charge states by clicking on the Label button. Note: It is likely that the automatic label optimiser is enabled and you can change that by clicking on the Customise plots... button and unchecking the Optimise label position option. Saving plots The easiest way to save any plot in ORIGAMI-ANALYSE is to plot it, customise it and then right-click in the plot area and select Save figure... . Note: It is likely that the figure will be automatically resized to a pre-defined image size. This can very occasionally cause problems, therefore you disable that option by unchecking the Resize on saving menu item. Saving data All deconvolution data is saved within the document and if you to the Document Tree and open-up the item (see below), you can right-click on any item and select the option Save results . If you click on the UniDec header, you can save all results at the same time. Plotting and replotting Find the desired item in the Document Tree and double-click on it to plot it.","title":"UniDec - deconvolution"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#unidec-deconvolution","text":"UniDec is a Bayesian deconvolution algorithm that can be used to deconvolute mass spectra and ion mobility-mass spectra. It was developed by Dr. Michael Marty and is freely available under the modified BSD licence. I would highly recommend you check-out UniDec (and MetaUniDec) software. If you use it in your work, please cite their work: M. T. Marty, A. J. Baldwin, E. G. Marklund, G. K. A. Hochberg, J. L. P. Benesch, C. V. Robinson, Anal. Chem. 2015, 87, 4370-4376.","title":"UniDec deconvolution"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#video-tutorial","text":"","title":"Video tutorial"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#deconvolution-in-origami-analyse","text":"Any mass spectrum within a ORIGAMI document can be deconvoluted and therefore a document can contain tens of spectra, each with its own deconvolution results. The easiest way to get started is to find an item in the Document Tree, right-click on it and select Deconvolute using UniDec... which will open a new panel where you can adjust the parameters.","title":"Deconvolution in ORIGAMI-ANALYSE"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#example-data","text":"In this example we will use a file provided with the ORIGAMI distribution. You can download MS file or you can find it in your ORIGAMI directory ( example_data/text ). This file contains a mass spectrum of a intrinsically disordered protein, p27 that is approx. 22.5 kDa in size and has a very broad charge state distribution.","title":"Example data"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#loading-data","text":"Please have a look at Loading Text files . In short, you either drag-and-drop the text file in the main window of ORIGAMI-ANALYSE or go to File - Open MS Text file .","title":"Loading data"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#deconvolution","text":"Once you've loaded data, right-click on it in the Document Tree and select Deconvolute using UniDec... If you are using the example file, you can start with the settings shown below: Specify Pre-processing parameters. You can start with m/z start = 500 and m/z end = 2500 with m/z bin size = 0.1 using Linear interpolation method. Click on the Pre-process button. If you are using the Tabbed view , the results will be shown in the tab UniDec - MS Specify deconvolution parameters. If you are unsure about the sample you are analysing, specify a broad range of charge states and the molecular weight with large-ish Sampling frequency. This will help you narrow down the appropriate range for your sample. Once you are happy, click on the Run UniDec button. If you are using the Tabbed view , the results will be shown in UniDec - m/z vs Charge / MW vs Charge / MW tabs. Following successful deconvolution, you can find peaks and identify the found molecular weights. To do this, specify appropriate parameters in the Peak detection parameters section and then click on the Detect peaks button. If you are using the Tabbed view , the results will be shown in UniDec - Isolated MS / Barplot tabs.","title":"Deconvolution"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#visualisation-of-results","text":"","title":"Visualisation of results"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#visualisation-of-individual-species","text":"If you are lucky, deconvolution will result in a single species being detect. This is rather unlikely and therefore you will be presented with a range of detected MW. In order to select and visualise only one species at at time, you can select an item with a molecular weight in the Dropdown menu (see below) and click on the Isolate button. You can also label its charge states by clicking on the Label button. Note: It is likely that the automatic label optimiser is enabled and you can change that by clicking on the Customise plots... button and unchecking the Optimise label position option.","title":"Visualisation of individual species"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#saving-plots","text":"The easiest way to save any plot in ORIGAMI-ANALYSE is to plot it, customise it and then right-click in the plot area and select Save figure... . Note: It is likely that the figure will be automatically resized to a pre-defined image size. This can very occasionally cause problems, therefore you disable that option by unchecking the Resize on saving menu item.","title":"Saving plots"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#saving-data","text":"All deconvolution data is saved within the document and if you to the Document Tree and open-up the item (see below), you can right-click on any item and select the option Save results . If you click on the UniDec header, you can save all results at the same time.","title":"Saving data"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#plotting-and-replotting","text":"Find the desired item in the Document Tree and double-click on it to plot it.","title":"Plotting and replotting"},{"location":"user-guide/interactive-output/simple-output.html","text":"Exporting interactive figures ORIGAMI enables creation of HTML/JavaScript webpages which embed interactive versions of figures visualised in ORIGAMI. Practically all figures that you can generate in the desktop application can be also exported to a HTML document that can be shared with your supervisor, journal reviewers or collaborators for their in-depth interrogation. While this might seem like a bit of a gimmick, it makes sense to share the results with the scientific community in a manner more explorative than a simple static image. See here for some helpful encouragement ( Perkel and Weissgerber ). Example In this example we will use a file provided with the ORIGAMI distribution. You can download MS file or you can find it in your ORIGAMI directory ( example_data/text ). Interactive output panel You can use any example file here as once you open the output window, all available plots will be shown in a list. In this case, the list contains all available items from a number of previous examples (e.g. annotating mass spectra, combining drift voltages, etc). If you click on any item in the list, its previously provided settings such as title, header, footnote information or plot parameters will be automatically rendered. Focusing on a mass spectrum first, you can see some useful information about the size of number of annotations, min/max ranges and its size . Check that item and click on the Export HTML button. You will be asked to provide a path where you would like to save the document. Make sure to check the Open in browser after saving checkbox. You can checkout a mass spectrum example here and heatmap example here .","title":"Getting started"},{"location":"user-guide/interactive-output/simple-output.html#exporting-interactive-figures","text":"ORIGAMI enables creation of HTML/JavaScript webpages which embed interactive versions of figures visualised in ORIGAMI. Practically all figures that you can generate in the desktop application can be also exported to a HTML document that can be shared with your supervisor, journal reviewers or collaborators for their in-depth interrogation. While this might seem like a bit of a gimmick, it makes sense to share the results with the scientific community in a manner more explorative than a simple static image. See here for some helpful encouragement ( Perkel and Weissgerber ).","title":"Exporting interactive figures"},{"location":"user-guide/interactive-output/simple-output.html#example","text":"In this example we will use a file provided with the ORIGAMI distribution. You can download MS file or you can find it in your ORIGAMI directory ( example_data/text ).","title":"Example"},{"location":"user-guide/interactive-output/simple-output.html#interactive-output-panel","text":"You can use any example file here as once you open the output window, all available plots will be shown in a list. In this case, the list contains all available items from a number of previous examples (e.g. annotating mass spectra, combining drift voltages, etc). If you click on any item in the list, its previously provided settings such as title, header, footnote information or plot parameters will be automatically rendered. Focusing on a mass spectrum first, you can see some useful information about the size of number of annotations, min/max ranges and its size . Check that item and click on the Export HTML button. You will be asked to provide a path where you would like to save the document. Make sure to check the Open in browser after saving checkbox. You can checkout a mass spectrum example here and heatmap example here .","title":"Interactive output panel"},{"location":"user-guide/processing/heatmaps.html","text":"Processing heatmaps All two-dimensional heatmaps can be processed to produce a more visually attractive figure. Video tutorial on how to process heatmaps Loading data Please have a look at Loading Text files . In short, you either drag-and-drop the text file in the main window of ORIGAMI-ANALYSE or go to File - Open IM-MS Text file . Example In this example we will use a file provided with the ORIGAMI distribution. You can download heatmap files or you can find them in your ORIGAMI directory ( example_data/text ). Opening processing panel The easiest way to process a heatmap is to find it in the Document Tree, right-click on it and select the Process... option. This will open a new window where you can select desired parameters and also execute the action. If you simply open the Processing window, it is not guaranteed ORIGAMI will know which heatmap you want to process, and will use the currently plotted heatmap as the data source. Of course, this is only a concern if you have more than one heatmap in the document. Processing Heatmaps can be processed in a number of ways, however the most common is to remove noise (using the threshold value) and normalize it (using the On/Off toggle). Setup your desired parameters and you can either replot the heatmap (data will not be added to the document) or process (data will be added to the document).","title":"Heatmap"},{"location":"user-guide/processing/heatmaps.html#processing-heatmaps","text":"All two-dimensional heatmaps can be processed to produce a more visually attractive figure.","title":"Processing heatmaps"},{"location":"user-guide/processing/heatmaps.html#video-tutorial-on-how-to-process-heatmaps","text":"","title":"Video tutorial on how to process heatmaps"},{"location":"user-guide/processing/heatmaps.html#loading-data","text":"Please have a look at Loading Text files . In short, you either drag-and-drop the text file in the main window of ORIGAMI-ANALYSE or go to File - Open IM-MS Text file .","title":"Loading data"},{"location":"user-guide/processing/heatmaps.html#example","text":"In this example we will use a file provided with the ORIGAMI distribution. You can download heatmap files or you can find them in your ORIGAMI directory ( example_data/text ).","title":"Example"},{"location":"user-guide/processing/heatmaps.html#opening-processing-panel","text":"The easiest way to process a heatmap is to find it in the Document Tree, right-click on it and select the Process... option. This will open a new window where you can select desired parameters and also execute the action. If you simply open the Processing window, it is not guaranteed ORIGAMI will know which heatmap you want to process, and will use the currently plotted heatmap as the data source. Of course, this is only a concern if you have more than one heatmap in the document.","title":"Opening processing panel"},{"location":"user-guide/processing/heatmaps.html#processing","text":"Heatmaps can be processed in a number of ways, however the most common is to remove noise (using the threshold value) and normalize it (using the On/Off toggle). Setup your desired parameters and you can either replot the heatmap (data will not be added to the document) or process (data will be added to the document).","title":"Processing"},{"location":"user-guide/processing/mass-spectra-annotation.html","text":"Annotating mass spectra Since version 1.1.2 it is possible to annotate mass spectra with custom labels (e.g. charge state , label ) and attached an arrow to highlight low-intensity species. Video tutorial on how to annotate mass spectrum Loading data Please have a look at Loading Text files . In short, you either drag-and-drop the text file in the main window of ORIGAMI-ANALYSE or go to File - Open MS Text file . Example In this example we will use a file provided with the ORIGAMI distribution. You can download MS file or you can find it in your ORIGAMI directory ( example_data/text ). Annotating There is a number of ways you can annote mass spectrum. The manual way involves opening an annotation panel and manually selecting peaks. You can also load annotations from a .csv file. Opening annotation panel Find the mass spectrum you would like to annotate in the Document Tree and right-click on it, then select Show annotations panel , a new window should show up: Adding an annotation Click on the Annotating: Off button so it switches to Annotating: On . Move your mouse to the mass spectrum window and hold CTRL on your keyboard while also dragging mouse over a peak (like during data extraction). When you release the mouse, a number of values will be added in the annotation panel (min/max band, position x, charge, intensity, etc) - all of which can be changed. When you are happy click on the Add annotation button. The annotation should appear in a list below. Repeat till you are fnished. Editing an annotation Select a annotation in the list below. Change any value. Click on the Add annotation button. Adding arrow to annotation Select a annotation in the list below. Uncheck the add arrow checkbox. Adjust values of position (x, label) and position (y, label) Click on the Add annotation button. Showing all annotations Click on the Show button and select appropriate option (e.g. Show m/z, intensity, charge). All annotations should be shown on the mass spectrum. Customising annotations You can adjust several parameters ( annotation color, arrow line thickness, label size, etc ) in the Customise annotations panel. You can open it by clicking on the Action button and selecting Customise other settings... . A new panel should open. Note: You will have to replot annotations as these settings do not automatically update. Duplicating annotations Sometimes you might have more than one mass spectrum a document that has a lot of the same peaks. You could manually re-add these, but there is a quicker way. Find the mass spectrum with annotations and right-click on it. Select Duplicate annotations... option. A new window will appear where you can select another document and mass spectrum to which annotations should be copied. Once you have selected, click Select and see if they have been copied. One thing to remember is that the intensity of the peaks in different peaks will vary so you have to fix the intensity of annotation label. To do this, open the annotation panel for newly copied annotations (Document Tree - Show annotations panel...) and click on the Action button. Once there, select Fix intensity option. Video tutorial on how to duplicate annotations","title":"Annotating mass spectra"},{"location":"user-guide/processing/mass-spectra-annotation.html#annotating-mass-spectra","text":"Since version 1.1.2 it is possible to annotate mass spectra with custom labels (e.g. charge state , label ) and attached an arrow to highlight low-intensity species.","title":"Annotating mass spectra"},{"location":"user-guide/processing/mass-spectra-annotation.html#video-tutorial-on-how-to-annotate-mass-spectrum","text":"","title":"Video tutorial on how to annotate mass spectrum"},{"location":"user-guide/processing/mass-spectra-annotation.html#loading-data","text":"Please have a look at Loading Text files . In short, you either drag-and-drop the text file in the main window of ORIGAMI-ANALYSE or go to File - Open MS Text file .","title":"Loading data"},{"location":"user-guide/processing/mass-spectra-annotation.html#example","text":"In this example we will use a file provided with the ORIGAMI distribution. You can download MS file or you can find it in your ORIGAMI directory ( example_data/text ).","title":"Example"},{"location":"user-guide/processing/mass-spectra-annotation.html#annotating","text":"There is a number of ways you can annote mass spectrum. The manual way involves opening an annotation panel and manually selecting peaks. You can also load annotations from a .csv file.","title":"Annotating"},{"location":"user-guide/processing/mass-spectra-annotation.html#opening-annotation-panel","text":"Find the mass spectrum you would like to annotate in the Document Tree and right-click on it, then select Show annotations panel , a new window should show up:","title":"Opening annotation panel"},{"location":"user-guide/processing/mass-spectra-annotation.html#adding-an-annotation","text":"Click on the Annotating: Off button so it switches to Annotating: On . Move your mouse to the mass spectrum window and hold CTRL on your keyboard while also dragging mouse over a peak (like during data extraction). When you release the mouse, a number of values will be added in the annotation panel (min/max band, position x, charge, intensity, etc) - all of which can be changed. When you are happy click on the Add annotation button. The annotation should appear in a list below. Repeat till you are fnished.","title":"Adding an annotation"},{"location":"user-guide/processing/mass-spectra-annotation.html#editing-an-annotation","text":"Select a annotation in the list below. Change any value. Click on the Add annotation button.","title":"Editing an annotation"},{"location":"user-guide/processing/mass-spectra-annotation.html#adding-arrow-to-annotation","text":"Select a annotation in the list below. Uncheck the add arrow checkbox. Adjust values of position (x, label) and position (y, label) Click on the Add annotation button.","title":"Adding arrow to annotation"},{"location":"user-guide/processing/mass-spectra-annotation.html#showing-all-annotations","text":"Click on the Show button and select appropriate option (e.g. Show m/z, intensity, charge). All annotations should be shown on the mass spectrum.","title":"Showing all annotations"},{"location":"user-guide/processing/mass-spectra-annotation.html#customising-annotations","text":"You can adjust several parameters ( annotation color, arrow line thickness, label size, etc ) in the Customise annotations panel. You can open it by clicking on the Action button and selecting Customise other settings... . A new panel should open. Note: You will have to replot annotations as these settings do not automatically update.","title":"Customising annotations"},{"location":"user-guide/processing/mass-spectra-annotation.html#duplicating-annotations","text":"Sometimes you might have more than one mass spectrum a document that has a lot of the same peaks. You could manually re-add these, but there is a quicker way. Find the mass spectrum with annotations and right-click on it. Select Duplicate annotations... option. A new window will appear where you can select another document and mass spectrum to which annotations should be copied. Once you have selected, click Select and see if they have been copied. One thing to remember is that the intensity of the peaks in different peaks will vary so you have to fix the intensity of annotation label. To do this, open the annotation panel for newly copied annotations (Document Tree - Show annotations panel...) and click on the Action button. Once there, select Fix intensity option.","title":"Duplicating annotations"},{"location":"user-guide/processing/mass-spectra-annotation.html#video-tutorial-on-how-to-duplicate-annotations","text":"","title":"Video tutorial on how to duplicate annotations"},{"location":"user-guide/processing/mass-spectra.html","text":"Processing mass spectra All mass spectra found in a ORIGAMI document can be processed in a way that reduced noise, smoothes peaks, or linearized the spectrum to reduce its size. Video tutorial on how to process mass spectra Loading data Please have a look at Loading Text files . In short, you either drag-and-drop the text file in the main window of ORIGAMI-ANALYSE or go to File - Open MS Text file . Example In this example we will use a file provided with the ORIGAMI distribution. You can download MS file or you can find it in your ORIGAMI directory ( example_data/text ). Raw mass spectrum Opening processing panel The easiest way to process a mass spectrum is to find it in the Document Tree, right-click on it and select the Process... option. This will open a new window where you can select desired parameters and also execute the action. If you simply open the Processing window, it is not guaranteed ORIGAMI will know which mass spectrum you want to process. Of course, this is only a concern if you have more than one spectrum in the document. Processing Spectral processing is taken in steps, and you can specify which action you would like to take. Crop spectrum: specify the min m/z and max m/z range spectrum should restricted to Linearize spectrum: linearize spectrum to have consistent spacing between points. There is a number of methods available that will change the way the spacing is calculated Smooth spectrum: specify the smoothing method (Gaussian or Savitzky-Golay) Baseline subtract: remove noise from the spectrum Normalize: normalize the spectrum to maximum value of 1 Once you are happy with your parameters, you can either replot the spectrum (data will not be added to the document) or process (data will be added to the document). Processed mass spectrum Note: If the Process button is disable, it probably means you just opened the Processing panel without specifying the mass spectrum - you can close it and try again from the Document Tree view.","title":"Mass spectrum"},{"location":"user-guide/processing/mass-spectra.html#processing-mass-spectra","text":"All mass spectra found in a ORIGAMI document can be processed in a way that reduced noise, smoothes peaks, or linearized the spectrum to reduce its size.","title":"Processing mass spectra"},{"location":"user-guide/processing/mass-spectra.html#video-tutorial-on-how-to-process-mass-spectra","text":"","title":"Video tutorial on how to process mass spectra"},{"location":"user-guide/processing/mass-spectra.html#loading-data","text":"Please have a look at Loading Text files . In short, you either drag-and-drop the text file in the main window of ORIGAMI-ANALYSE or go to File - Open MS Text file .","title":"Loading data"},{"location":"user-guide/processing/mass-spectra.html#example","text":"In this example we will use a file provided with the ORIGAMI distribution. You can download MS file or you can find it in your ORIGAMI directory ( example_data/text ). Raw mass spectrum","title":"Example"},{"location":"user-guide/processing/mass-spectra.html#opening-processing-panel","text":"The easiest way to process a mass spectrum is to find it in the Document Tree, right-click on it and select the Process... option. This will open a new window where you can select desired parameters and also execute the action. If you simply open the Processing window, it is not guaranteed ORIGAMI will know which mass spectrum you want to process. Of course, this is only a concern if you have more than one spectrum in the document.","title":"Opening processing panel"},{"location":"user-guide/processing/mass-spectra.html#processing","text":"Spectral processing is taken in steps, and you can specify which action you would like to take. Crop spectrum: specify the min m/z and max m/z range spectrum should restricted to Linearize spectrum: linearize spectrum to have consistent spacing between points. There is a number of methods available that will change the way the spacing is calculated Smooth spectrum: specify the smoothing method (Gaussian or Savitzky-Golay) Baseline subtract: remove noise from the spectrum Normalize: normalize the spectrum to maximum value of 1 Once you are happy with your parameters, you can either replot the spectrum (data will not be added to the document) or process (data will be added to the document). Processed mass spectrum Note: If the Process button is disable, it probably means you just opened the Processing panel without specifying the mass spectrum - you can close it and try again from the Document Tree view.","title":"Processing"}]}
\ No newline at end of file
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Main features Import single or multiple files (requires Driftscope for Waters .raw) Batch data extraction, processing and exporting Easy analysis and visualisation of aIM/CIU/SID datasets Highly customisable graphical environment to make high-quality figures Built-in CCS calibration and DT-IMS analysis Added functionality via plugins (e.g. UniDec deconvolution) Export all possible figures in an interactive .html document Getting started See the installation guide for instructions on how to get started. Examples A number of example files have been provided to get started! Please see various user guides and the examples page for more information. Main window","title":"Home"},{"location":"index.html#home","text":"","title":"Home"},{"location":"index.html#about","text":"ORIGAMI-ANALYSE is a data processing and visualisation software The analysis software, ORIGAMI-ANALYSE can aid analysis of MS and IM-MS results from multiple instrumental platforms, offering rich data extraction, data processing and visualisation environment. Data can be imported from text (.csv/.txt/.tab), tandem MS (.mgf/.mzML/.mzIdent) and raw files (Waters .raw). ORIGAMI-ANALYSE was developed to handle a large number of files simultaneously, providing comparative and interactive environment to visualise results from multiple resources, generate publication-quality figures and interpret the results in more depth. All the processed data can be also exported as an interactive .html document that can be visualised in a web-browser and shared with your colleagues, reviewers or editors, as well as included as an SI.","title":"About"},{"location":"index.html#main-features","text":"Import single or multiple files (requires Driftscope for Waters .raw) Batch data extraction, processing and exporting Easy analysis and visualisation of aIM/CIU/SID datasets Highly customisable graphical environment to make high-quality figures Built-in CCS calibration and DT-IMS analysis Added functionality via plugins (e.g. UniDec deconvolution) Export all possible figures in an interactive .html document","title":"Main features"},{"location":"index.html#getting-started","text":"See the installation guide for instructions on how to get started.","title":"Getting started"},{"location":"index.html#examples","text":"A number of example files have been provided to get started! Please see various user guides and the examples page for more information.","title":"Examples"},{"location":"index.html#main-window","text":"","title":"Main window"},{"location":"changelog/v1.2.0.3-5-11-2018.html","text":"Changes made in v1.2.0.3 General The underlying codebase of ORIGAMI has been improved to make it more readable and more responsive Item font color will be automatically adjusted to ensure best contrast from the background color in various lists in the GUI Logging of events was temporarily disabled as it appears to be causing some issues. I haven't been able to figure out why it crashes the program (yet). Tandem MS :star Added support to load .mgf and .mzIdentML file formats to visualise tandem mass spectrometry results. Menu - Open open-source files... to load .mgf files. You can then annotate the tandem MS with peptide fragments. See Figure 1 for example. Interactive panel Started adding support for individual modification of parameters for interactive plots (double-clicking on an item in the list) Issue that prevent proper showing of toolbar has been removed Peaklist panel Added 'Extract automatically' check tool (Peaklist - Toolbar - Extract...) Added a lot of new shortcuts for easier plotting Text file panel Added 'Extract automatically' check tool (Peaklist - Toolbar - Extract...) Removed an issue that would incorrectly remove documents from the text file list Multiple MS files panel The average mass spectrum can be re-binned/re-processed based on new parameters (Process - Average mass spectra (current document)) Removed an issue that prevented typing-in numerical values in the 'variable' colument when using laptop keyboards. I have only ever encountered this issue once... Let me know if it still occurs! Document tree Double-clicking on the document header will now clear all plots and show the most basic plots for that document (e.g. MS, DT, RT, etc). You can also do this by Right-click - Refresh document. Significant improvements to the right-click menus (most notably for UniDec/Annotations) Plots panel Some images can now be rotated by 90 degrees (mainly 2D) Wheel-zoom in the X-dimensions has been improved (works like on maps now) Data extraction You can now extract mass spectra from the '2D' panel. Hold CTRL on your keyboard and drag the mouse in the plot area. Only works when standard plot is shown (e.g. Drift time (bins) vs Scans/Time) Extracted mass spectra extracted in the DT and RT windows will be now shown in an area beneath the extraction plot (for convenience) MS annotations Peaks can now be annotated with an arrow (also available when exporting in an interactive format) Selection of a peak in the MS window using the mouse (Annotating: On) will automatically try to determine the charge state based on the peaks isotopic distribution. You can change the error tolerance in Action - Customise other settings - Charge prediction value (default: 0.05). UniDec settings Plots can now be customised using settings editor. (Settings: UniDec - Customise plots...) You can switch between tabbed view where each plot is in a separate tab OR continuous view where all plots are available on the same page (Customise plots... - Panel view) Deconvolution is now done in a multi-threaded mode. Should stop program from hanging All deconvolution results will be now stored in a temporary_data folder (found in ORIGAMI directory). This should keep your HDDs a little bit tidier. All files will be deleted at the end of the session. MS comparison You can now assign your own label to the plot. You can now compare ALL available mass spectra and not just those that were hidden under 'Mass Spectra' tag. (This includes: Mass Spectra, Mass Spectrum, Mass Spectrum (processed)). To open comparison panel: Menu - View - Open MS comparison panel...) Peak detection Works in multi-threaded mode. Should stop program from hanging.","title":"v1.2.0.3 - 7/11/2018"},{"location":"changelog/v1.2.0.3-5-11-2018.html#changes-made-in-v1203","text":"","title":"Changes made in v1.2.0.3"},{"location":"changelog/v1.2.0.3-5-11-2018.html#general","text":"The underlying codebase of ORIGAMI has been improved to make it more readable and more responsive Item font color will be automatically adjusted to ensure best contrast from the background color in various lists in the GUI Logging of events was temporarily disabled as it appears to be causing some issues. I haven't been able to figure out why it crashes the program (yet).","title":"General"},{"location":"changelog/v1.2.0.3-5-11-2018.html#tandem-ms-star","text":"Added support to load .mgf and .mzIdentML file formats to visualise tandem mass spectrometry results. Menu - Open open-source files... to load .mgf files. You can then annotate the tandem MS with peptide fragments. See Figure 1 for example.","title":"Tandem MS :star"},{"location":"changelog/v1.2.0.3-5-11-2018.html#interactive-panel","text":"Started adding support for individual modification of parameters for interactive plots (double-clicking on an item in the list) Issue that prevent proper showing of toolbar has been removed","title":"Interactive panel"},{"location":"changelog/v1.2.0.3-5-11-2018.html#peaklist-panel","text":"Added 'Extract automatically' check tool (Peaklist - Toolbar - Extract...) Added a lot of new shortcuts for easier plotting","title":"Peaklist panel"},{"location":"changelog/v1.2.0.3-5-11-2018.html#text-file-panel","text":"Added 'Extract automatically' check tool (Peaklist - Toolbar - Extract...) Removed an issue that would incorrectly remove documents from the text file list","title":"Text file panel"},{"location":"changelog/v1.2.0.3-5-11-2018.html#multiple-ms-files-panel","text":"The average mass spectrum can be re-binned/re-processed based on new parameters (Process - Average mass spectra (current document)) Removed an issue that prevented typing-in numerical values in the 'variable' colument when using laptop keyboards. I have only ever encountered this issue once... Let me know if it still occurs!","title":"Multiple MS files panel"},{"location":"changelog/v1.2.0.3-5-11-2018.html#document-tree","text":"Double-clicking on the document header will now clear all plots and show the most basic plots for that document (e.g. MS, DT, RT, etc). You can also do this by Right-click - Refresh document. Significant improvements to the right-click menus (most notably for UniDec/Annotations)","title":"Document tree"},{"location":"changelog/v1.2.0.3-5-11-2018.html#plots-panel","text":"Some images can now be rotated by 90 degrees (mainly 2D) Wheel-zoom in the X-dimensions has been improved (works like on maps now)","title":"Plots panel"},{"location":"changelog/v1.2.0.3-5-11-2018.html#data-extraction","text":"You can now extract mass spectra from the '2D' panel. Hold CTRL on your keyboard and drag the mouse in the plot area. Only works when standard plot is shown (e.g. Drift time (bins) vs Scans/Time) Extracted mass spectra extracted in the DT and RT windows will be now shown in an area beneath the extraction plot (for convenience)","title":"Data extraction"},{"location":"changelog/v1.2.0.3-5-11-2018.html#ms-annotations","text":"Peaks can now be annotated with an arrow (also available when exporting in an interactive format) Selection of a peak in the MS window using the mouse (Annotating: On) will automatically try to determine the charge state based on the peaks isotopic distribution. You can change the error tolerance in Action - Customise other settings - Charge prediction value (default: 0.05).","title":"MS annotations"},{"location":"changelog/v1.2.0.3-5-11-2018.html#unidec-settings","text":"Plots can now be customised using settings editor. (Settings: UniDec - Customise plots...) You can switch between tabbed view where each plot is in a separate tab OR continuous view where all plots are available on the same page (Customise plots... - Panel view) Deconvolution is now done in a multi-threaded mode. Should stop program from hanging All deconvolution results will be now stored in a temporary_data folder (found in ORIGAMI directory). This should keep your HDDs a little bit tidier. All files will be deleted at the end of the session.","title":"UniDec settings"},{"location":"changelog/v1.2.0.3-5-11-2018.html#ms-comparison","text":"You can now assign your own label to the plot. You can now compare ALL available mass spectra and not just those that were hidden under 'Mass Spectra' tag. (This includes: Mass Spectra, Mass Spectrum, Mass Spectrum (processed)). To open comparison panel: Menu - View - Open MS comparison panel...)","title":"MS comparison"},{"location":"changelog/v1.2.0.3-5-11-2018.html#peak-detection","text":"Works in multi-threaded mode. Should stop program from hanging.","title":"Peak detection"},{"location":"changelog/v1.2.1.4-9-1-2019.html","text":"What changed in ORIGAMI ANALYSE Documentation Added online documentation Added several new videos to the YouTube playlist Document Tree Fixed typo: spectrun - spectrum (grr) When loading mzml/mgf files, the individual scans will no longer be shown in the document tree as it caused some major issues. If you would like to see the individual spectra, please double-click on the header 'Tandem Mass Spectra' Fixed a problem when trying to plot waterfall plot from the Document Tree menu When loading any data into the INTERACTIVE document, you will be asked whether data should be duplicated, merged or duplicated When plotting a waterfall plot, data will be checked to ensure its not too big (e.g. not too many rows). If the value is above the threshold (set to 500), you will be asked if you would like to continue Main window Added new menu: Plugins . This menu will hold all future mini-applications Umder the menu Plot settings I've added a couple new options that allow modification of plot extra plot parameters. The help pages (Help - Help pages - ...) have now been replaced with links to the new documentation (opens in the browser). Where no documentation exists yet, old pages will be shown. Also available online Annotations you can now also easily 'duplicate/multiply' annotations. Action - Multiply annotations... this will result in a copy of the selected annotation(s) with slight difference in the min-value (so they can be distinguished from its parent) Text annotations can now be added to other plots (scatter, v-bar, h-bar, waterfall, multi-line/overlay). To added annotations, find it in the Document Tree , right-click on it and you should be presented with option Show annotations panel... . Then you can simply follow the standard annotations protocol. See here for more information Annotations parameters can now be easily modified as they can be dragged on the plot. If an annotation is shown on your plot, you can simply drag it around in the plot area and once you let-go, new settings (e.g. position) will be updated in the ORIGAMI document. font size, weight and rotation will now be aplied when adding labels auto-label generator will now also create labels based purely on the charge state annotation parameters (e.g. size, weight, rotation) will be respected when replotting from the Document Tree Interactive panel Made big progres in terms of copying/applying styles for plot elements. When you double-click on any element in the file list a new window will appear where you can individually adjust plot parameters. When you finished, you can right-click on that same (or any other) item in the list and select 'Copy style..'. You can then select any other item in the list, right-click on it and select 'Apply style..'. certain plot types (v-bar, h-bar, scatter, waterfall, multi-line/overlay) will now support addition of annotations (and their widgets). Annotations can correspond to anything you wish to say about specific region of a dataset. Scatter plots that are created from datasets loaded through text files with added metadata can be enhanced with weblinks/URLs. See the example for more information. fixed sorting in the list (especilaly when using the 'Show selected' option) Lists are sorted using 'natural sorting' from now on, meaning they should be more logically sorted. fixed the show/hide table elements when you right-click on the table headers Colorbars: added loads of new settings users can control better behaviour when adding colorbars to plots removed tools/toolset from ORIGAMI - the new system of copy/apply style should work much better I've realised that using 'coffeescript' for widget exportation was a big mistake as it takes ~10x+ longer to compile that script than pure JavaScript. Adding widgets will be a lot faster from now on (a couple haven't been ported to JS yet). Plots Improved color handling in violin and waterfall plots. The line color (edge) and shade/fill-under can be independently controlled now. UVPD processing Added new plug that allows analysis and processing of UVPD datasets that were acquired with laser being constantly switched on/off. This is a user-specific plugin that will most likely have no use for anyone else apart from some Barran group members. To activate, click on the Menu - Plugins - UVPD processing window... . Tandem MS panel You can now load .mzML files (haven't figured out how to add .mzIdentML files to them yet...) MS/MS files can now be exported in an interactive format (.html document). This feature is still in development and I imagine will not be stable until v1.2.2 at the earliest. At the moment, individual scans of MS/MS file (.mgf only) can be annotated (e.g. fragments can be generated) and added to the file. Scans that have been user-annotated can be subsequently exported. This will be properly showcased in a tutorial. Added two new options in the Action menu which permit improved population of the table by either excluding scans with PTMs and excluding scans without identification. Clicking on either of these will automatically trigger re-population of the table based on the selected options. You can see what PTMs have been included in the scan by clicking on the Modifications list Scans that have multiple identification information will be separated into separae instances in the table (e.g. look at the column ID #) Fragment generator can now handle PTMs (at least those that have kept the mass information) Improved the way scans are loaded (faster and actually works...) Improved the way butterfly plots are shown. A horizontal line will be drawn from now on (at y=0) Added several new customisation parameters that permit better data visualisation. These are found under Action - Customise... When selecting frag-all option, appropriate checkboxes will be ticked from now on Fixed fragment generator to stop overriding fragments with same name (e.g. y1+ was equal y_H2Ox11+...) Other data - Annotated data Added new keyword 'axis_url'/'axis_urls' to the data parser. These keywords can be used to provide web addresses which can be attached to the data (scatter points only for now). If valid URL address is provided, when you tap on a point you will be taken to a new tab in your browser which corresponds to the web address. This is only valid in the interactive plots Changed the poorly selected name of 'Other data' to 'Annotated data' Figures Updated MS/MS panel MS/MS customisation window Annotated MS/MS mass spectrum with automatically generated arrows Interactive data customisation window Interactive copy style Animation Interactive adjustment of labels Mailing list If you would like to be added to the ORIGAMI mailing list where you will be notified of new releases, please contact lukasz.migas@manchester.ac.uk or visit ORIGAMI documentation website . How to update A lot has changed in this version so the only way to update is to download the package and unpack it somewhere else on your PC. I've tried really hard not to break too many things :) Many thanks, Lukasz","title":"v1.2.1.1 - 27/12/2018"},{"location":"changelog/v1.2.1.4-9-1-2019.html#what-changed-in-origamianalyse","text":"","title":"What changed in ORIGAMIANALYSE"},{"location":"changelog/v1.2.1.4-9-1-2019.html#documentation","text":"Added online documentation Added several new videos to the YouTube playlist","title":"Documentation"},{"location":"changelog/v1.2.1.4-9-1-2019.html#document-tree","text":"Fixed typo: spectrun - spectrum (grr) When loading mzml/mgf files, the individual scans will no longer be shown in the document tree as it caused some major issues. If you would like to see the individual spectra, please double-click on the header 'Tandem Mass Spectra' Fixed a problem when trying to plot waterfall plot from the Document Tree menu When loading any data into the INTERACTIVE document, you will be asked whether data should be duplicated, merged or duplicated When plotting a waterfall plot, data will be checked to ensure its not too big (e.g. not too many rows). If the value is above the threshold (set to 500), you will be asked if you would like to continue","title":"Document Tree"},{"location":"changelog/v1.2.1.4-9-1-2019.html#main-window","text":"Added new menu: Plugins . This menu will hold all future mini-applications Umder the menu Plot settings I've added a couple new options that allow modification of plot extra plot parameters. The help pages (Help - Help pages - ...) have now been replaced with links to the new documentation (opens in the browser). Where no documentation exists yet, old pages will be shown. Also available online","title":"Main window"},{"location":"changelog/v1.2.1.4-9-1-2019.html#annotations","text":"you can now also easily 'duplicate/multiply' annotations. Action - Multiply annotations... this will result in a copy of the selected annotation(s) with slight difference in the min-value (so they can be distinguished from its parent) Text annotations can now be added to other plots (scatter, v-bar, h-bar, waterfall, multi-line/overlay). To added annotations, find it in the Document Tree , right-click on it and you should be presented with option Show annotations panel... . Then you can simply follow the standard annotations protocol. See here for more information Annotations parameters can now be easily modified as they can be dragged on the plot. If an annotation is shown on your plot, you can simply drag it around in the plot area and once you let-go, new settings (e.g. position) will be updated in the ORIGAMI document. font size, weight and rotation will now be aplied when adding labels auto-label generator will now also create labels based purely on the charge state annotation parameters (e.g. size, weight, rotation) will be respected when replotting from the Document Tree","title":"Annotations"},{"location":"changelog/v1.2.1.4-9-1-2019.html#interactive-panel","text":"Made big progres in terms of copying/applying styles for plot elements. When you double-click on any element in the file list a new window will appear where you can individually adjust plot parameters. When you finished, you can right-click on that same (or any other) item in the list and select 'Copy style..'. You can then select any other item in the list, right-click on it and select 'Apply style..'. certain plot types (v-bar, h-bar, scatter, waterfall, multi-line/overlay) will now support addition of annotations (and their widgets). Annotations can correspond to anything you wish to say about specific region of a dataset. Scatter plots that are created from datasets loaded through text files with added metadata can be enhanced with weblinks/URLs. See the example for more information. fixed sorting in the list (especilaly when using the 'Show selected' option) Lists are sorted using 'natural sorting' from now on, meaning they should be more logically sorted. fixed the show/hide table elements when you right-click on the table headers Colorbars: added loads of new settings users can control better behaviour when adding colorbars to plots removed tools/toolset from ORIGAMI - the new system of copy/apply style should work much better I've realised that using 'coffeescript' for widget exportation was a big mistake as it takes ~10x+ longer to compile that script than pure JavaScript. Adding widgets will be a lot faster from now on (a couple haven't been ported to JS yet).","title":"Interactive panel"},{"location":"changelog/v1.2.1.4-9-1-2019.html#plots","text":"Improved color handling in violin and waterfall plots. The line color (edge) and shade/fill-under can be independently controlled now.","title":"Plots"},{"location":"changelog/v1.2.1.4-9-1-2019.html#uvpd-processing","text":"Added new plug that allows analysis and processing of UVPD datasets that were acquired with laser being constantly switched on/off. This is a user-specific plugin that will most likely have no use for anyone else apart from some Barran group members. To activate, click on the Menu - Plugins - UVPD processing window... .","title":"UVPD processing"},{"location":"changelog/v1.2.1.4-9-1-2019.html#tandem-ms-panel","text":"You can now load .mzML files (haven't figured out how to add .mzIdentML files to them yet...) MS/MS files can now be exported in an interactive format (.html document). This feature is still in development and I imagine will not be stable until v1.2.2 at the earliest. At the moment, individual scans of MS/MS file (.mgf only) can be annotated (e.g. fragments can be generated) and added to the file. Scans that have been user-annotated can be subsequently exported. This will be properly showcased in a tutorial. Added two new options in the Action menu which permit improved population of the table by either excluding scans with PTMs and excluding scans without identification. Clicking on either of these will automatically trigger re-population of the table based on the selected options. You can see what PTMs have been included in the scan by clicking on the Modifications list Scans that have multiple identification information will be separated into separae instances in the table (e.g. look at the column ID #) Fragment generator can now handle PTMs (at least those that have kept the mass information) Improved the way scans are loaded (faster and actually works...) Improved the way butterfly plots are shown. A horizontal line will be drawn from now on (at y=0) Added several new customisation parameters that permit better data visualisation. These are found under Action - Customise... When selecting frag-all option, appropriate checkboxes will be ticked from now on Fixed fragment generator to stop overriding fragments with same name (e.g. y1+ was equal y_H2Ox11+...)","title":"Tandem MS panel"},{"location":"changelog/v1.2.1.4-9-1-2019.html#other-data-annotated-data","text":"Added new keyword 'axis_url'/'axis_urls' to the data parser. These keywords can be used to provide web addresses which can be attached to the data (scatter points only for now). If valid URL address is provided, when you tap on a point you will be taken to a new tab in your browser which corresponds to the web address. This is only valid in the interactive plots Changed the poorly selected name of 'Other data' to 'Annotated data'","title":"Other data -&gt; Annotated data"},{"location":"changelog/v1.2.1.4-9-1-2019.html#figures","text":"Updated MS/MS panel MS/MS customisation window Annotated MS/MS mass spectrum with automatically generated arrows Interactive data customisation window Interactive copy style","title":"Figures"},{"location":"changelog/v1.2.1.4-9-1-2019.html#animation","text":"Interactive adjustment of labels","title":"Animation"},{"location":"changelog/v1.2.1.4-9-1-2019.html#mailing-list","text":"If you would like to be added to the ORIGAMI mailing list where you will be notified of new releases, please contact lukasz.migas@manchester.ac.uk or visit ORIGAMI documentation website .","title":"Mailing list"},{"location":"changelog/v1.2.1.4-9-1-2019.html#how-to-update","text":"A lot has changed in this version so the only way to update is to download the package and unpack it somewhere else on your PC. I've tried really hard not to break too many things :) Many thanks, Lukasz","title":"How to update"},{"location":"interactive-examples/ccs-compendium.html","text":"Interactive scatter plot Some background I recently came across this nice paper from John McLean's lab at Vanderbilt which discusses how we can use a relatively large (~4000 values) database of measured standards in omics studies. They have created a R Shiny app which provides interactivity to explore the dataset. Since I have been recently improving ORIGAMI's interactive capabilities, I've decided to embed their dataset in ORIGAMI and export it as a self-sufficient HTML document. This took me about ~10 minutes altogether (mostly rearranging columns and annotating text document). I think the results are quite close to the original publication (Figure 2a). See figure in another tab Interactive figure Formatted data You can have a look at the way the data is structured below. Download formatted data You can download the data used for this figure from here .","title":"CCS compendium"},{"location":"interactive-examples/ccs-compendium.html#interactive-scatter-plot","text":"","title":"Interactive scatter plot"},{"location":"interactive-examples/ccs-compendium.html#some-background","text":"I recently came across this nice paper from John McLean's lab at Vanderbilt which discusses how we can use a relatively large (~4000 values) database of measured standards in omics studies. They have created a R Shiny app which provides interactivity to explore the dataset. Since I have been recently improving ORIGAMI's interactive capabilities, I've decided to embed their dataset in ORIGAMI and export it as a self-sufficient HTML document. This took me about ~10 minutes altogether (mostly rearranging columns and annotating text document). I think the results are quite close to the original publication (Figure 2a). See figure in another tab","title":"Some background"},{"location":"interactive-examples/ccs-compendium.html#interactive-figure","text":"","title":"Interactive figure"},{"location":"interactive-examples/ccs-compendium.html#formatted-data","text":"You can have a look at the way the data is structured below.","title":"Formatted data"},{"location":"interactive-examples/ccs-compendium.html#download-formatted-data","text":"You can download the data used for this figure from here .","title":"Download formatted data"},{"location":"interactive-examples/heatmap.html","text":"Interactive heatmap Figures without widgets You can easily export heatmaps and share them with the scientific world! See figure in another tab Figure with widgets You can also annotate figure with multiple widgets that can improve the visualisation experience. It might be desirable to give readers/consumers the possibility to adjust the figure to their preferences. The example below shows how the colormap of the figure can be adjusted to bee more colorblind friendly and the reader can change the colormap too. See figure in another tab","title":"Heatmap"},{"location":"interactive-examples/heatmap.html#interactive-heatmap","text":"","title":"Interactive heatmap"},{"location":"interactive-examples/heatmap.html#figures-without-widgets","text":"You can easily export heatmaps and share them with the scientific world! See figure in another tab","title":"Figures without widgets"},{"location":"interactive-examples/heatmap.html#figure-with-widgets","text":"You can also annotate figure with multiple widgets that can improve the visualisation experience. It might be desirable to give readers/consumers the possibility to adjust the figure to their preferences. The example below shows how the colormap of the figure can be adjusted to bee more colorblind friendly and the reader can change the colormap too. See figure in another tab","title":"Figure with widgets"},{"location":"interactive-examples/mass-spectrum.html","text":"Interactive mass spectrum Figures without widgets You can easily export annotated mass spectrum and share it with the scientific world! Here is an example of a mass spectrum of a NIST antibody that you can zoom-in, move around, hover-over and more. See figure in another tab Figure with widgets You can also annotate figure with multiple widgets that can improve the visualisation experience. It might be desirable to give readers/consumers the possibility to adjust the figure to their preferences. The example below shows how labels can be removed, their size can be adjusted and the behaviour of the hover tool can be altered. See figure in another tab","title":"Mass spectrum"},{"location":"interactive-examples/mass-spectrum.html#interactive-mass-spectrum","text":"","title":"Interactive mass spectrum"},{"location":"interactive-examples/mass-spectrum.html#figures-without-widgets","text":"You can easily export annotated mass spectrum and share it with the scientific world! Here is an example of a mass spectrum of a NIST antibody that you can zoom-in, move around, hover-over and more. See figure in another tab","title":"Figures without widgets"},{"location":"interactive-examples/mass-spectrum.html#figure-with-widgets","text":"You can also annotate figure with multiple widgets that can improve the visualisation experience. It might be desirable to give readers/consumers the possibility to adjust the figure to their preferences. The example below shows how labels can be removed, their size can be adjusted and the behaviour of the hover tool can be altered. See figure in another tab","title":"Figure with widgets"},{"location":"interactive-examples/protemics-scans.html","text":"Interactive MS/MS spectra Some background Somewhat inspired by xiSPEC to bring proteomics data to the webbrowser, I've slowly been adding functionality to load and annotate MS/MS data. ORIGAMI can currently read .mgf and .mzml files as well as .mzid files. The mzIdentML files can be used as source of annotations (results) of the .mgf files (NOT .mzml...). When you load load a .mgf file, it will typically include 100s to 1000s of scans, each of which will contain 10s to 100s of peaks. The .mgf file does not store any annotation information (apart from precursor m/z, charge and a couple of other software specific annotations) so it must be supplemented with a .mzid file. In the example that I've used, the .mgf file contains ~4000 scans and when the .mzid file is loaded, each is annotated with appropriate peptide information and associated post-translational modification information. I have randomly selected a couple of scans and annotated them using the built-in fragment predictor (based on user-defined parameters) and as you can see below, when you select a scan, each 'dataset' includes data about the precursor (charge, peptide sequence, start/end position) and protein (including accession ID and protein sequence). In the current implementation, PTM information is not displayed below the plot, however is considered when generating fragments. Actions: Dropdown menu: Select dataset you are interested in Drag: Zoom-in on any plot area Hover: Discover information about peak including m/z, intensity, charge, fragment label, error, peptide sequence, modification See figure in another tab Interactive figure","title":"Proteomics - MS/MS"},{"location":"interactive-examples/protemics-scans.html#interactive-msms-spectra","text":"","title":"Interactive MS/MS spectra"},{"location":"interactive-examples/protemics-scans.html#some-background","text":"Somewhat inspired by xiSPEC to bring proteomics data to the webbrowser, I've slowly been adding functionality to load and annotate MS/MS data. ORIGAMI can currently read .mgf and .mzml files as well as .mzid files. The mzIdentML files can be used as source of annotations (results) of the .mgf files (NOT .mzml...). When you load load a .mgf file, it will typically include 100s to 1000s of scans, each of which will contain 10s to 100s of peaks. The .mgf file does not store any annotation information (apart from precursor m/z, charge and a couple of other software specific annotations) so it must be supplemented with a .mzid file. In the example that I've used, the .mgf file contains ~4000 scans and when the .mzid file is loaded, each is annotated with appropriate peptide information and associated post-translational modification information. I have randomly selected a couple of scans and annotated them using the built-in fragment predictor (based on user-defined parameters) and as you can see below, when you select a scan, each 'dataset' includes data about the precursor (charge, peptide sequence, start/end position) and protein (including accession ID and protein sequence). In the current implementation, PTM information is not displayed below the plot, however is considered when generating fragments. Actions: Dropdown menu: Select dataset you are interested in Drag: Zoom-in on any plot area Hover: Discover information about peak including m/z, intensity, charge, fragment label, error, peptide sequence, modification See figure in another tab","title":"Some background"},{"location":"interactive-examples/protemics-scans.html#interactive-figure","text":"","title":"Interactive figure"},{"location":"main/about.html","text":"About Author Lukasz G. Migas | Website | GitHub Getting in touch If you have any questions, encounter problems or would like to chat, please contact Lukasz Migas (lukasz.migas@manchester.ac.uk or lukas.migas@yahoo.com or @munieq11 ). Contributors Prof. Perdita E. Barran Bruno Bellina Aidan France Florian Benoit","title":"About"},{"location":"main/about.html#about","text":"","title":"About"},{"location":"main/about.html#author","text":"Lukasz G. Migas | Website | GitHub","title":"Author"},{"location":"main/about.html#getting-in-touch","text":"If you have any questions, encounter problems or would like to chat, please contact Lukasz Migas (lukasz.migas@manchester.ac.uk or lukas.migas@yahoo.com or @munieq11 ).","title":"Getting in touch"},{"location":"main/about.html#contributors","text":"Prof. Perdita E. Barran Bruno Bellina Aidan France Florian Benoit","title":"Contributors"},{"location":"main/bugs.html","text":"Report Bugs Go to the Google Forms If you've encountered any issues, please use this form to report them.","title":"Report Bugs"},{"location":"main/bugs.html#report-bugs","text":"","title":"Report Bugs"},{"location":"main/bugs.html#go-to-the-google-forms","text":"If you've encountered any issues, please use this form to report them.","title":"Go to the Google Forms"},{"location":"main/cite.html","text":"Citation Reference If you use ORIGAMI, please consider citing it in your work: L. G. Migas, A. P. France, B. Bellina, P. E. Barran, \"ORIGAMI: A software suite for activated ion mobility mass spectrometry (aIM-MS) applied to multimeric protein assemblies\u201d, Int. J. Mass Spectrom., 2017 RIS TY - JOUR T1 - ORIGAMI: A software suite for activated ion mobility mass spectrometry (aIM-MS) applied to multimeric protein assemblies AU - Migas, Lukasz G. AU - France, Aidan P. AU - Bellina, Bruno AU - Barran, Perdita E. JO - International Journal of Mass Spectrometry VL - 427 SP - 20 EP - 28 PY - 2018 DA - 2018/04/01/ T2 - Richard Smith Honor Issue SN - 1387-3806 DO - https://doi.org/10.1016/j.ijms.2017.08.014 UR - http://www.sciencedirect.com/science/article/pii/S1387380617302695 KW - Collision induced dissociation (CID) KW - Collision induced unfolding (CIU) KW - Activated ion mobility (aIM) KW - Ion mobility (IM) KW - Mass spectrometry (MS) KW - Software KW - Python AB - ER - BibTex @article{MIGAS201820, title = ORIGAMI: A software suite for activated ion mobility mass spectrometry (aIM-MS) applied to multimeric protein assemblies , journal = International Journal of Mass Spectrometry , volume = 427 , pages = 20 - 28 , year = 2018 , note = Richard Smith Honor Issue , issn = 1387-3806 , doi = https://doi.org/10.1016/j.ijms.2017.08.014 , url = http://www.sciencedirect.com/science/article/pii/S1387380617302695 , author = Lukasz G. Migas and Aidan P. France and Bruno Bellina and Perdita E. Barran , keywords = Collision induced dissociation (CID), Collision induced unfolding (CIU), Activated ion mobility (aIM), Ion mobility (IM), Mass spectrometry (MS), Software, Python }","title":"Cite"},{"location":"main/cite.html#citation","text":"","title":"Citation"},{"location":"main/cite.html#reference","text":"If you use ORIGAMI, please consider citing it in your work: L. G. Migas, A. P. France, B. Bellina, P. E. Barran, \"ORIGAMI: A software suite for activated ion mobility mass spectrometry (aIM-MS) applied to multimeric protein assemblies\u201d, Int. J. Mass Spectrom., 2017","title":"Reference"},{"location":"main/cite.html#ris","text":"TY - JOUR T1 - ORIGAMI: A software suite for activated ion mobility mass spectrometry (aIM-MS) applied to multimeric protein assemblies AU - Migas, Lukasz G. AU - France, Aidan P. AU - Bellina, Bruno AU - Barran, Perdita E. JO - International Journal of Mass Spectrometry VL - 427 SP - 20 EP - 28 PY - 2018 DA - 2018/04/01/ T2 - Richard Smith Honor Issue SN - 1387-3806 DO - https://doi.org/10.1016/j.ijms.2017.08.014 UR - http://www.sciencedirect.com/science/article/pii/S1387380617302695 KW - Collision induced dissociation (CID) KW - Collision induced unfolding (CIU) KW - Activated ion mobility (aIM) KW - Ion mobility (IM) KW - Mass spectrometry (MS) KW - Software KW - Python AB - ER -","title":"RIS"},{"location":"main/cite.html#bibtex","text":"@article{MIGAS201820, title = ORIGAMI: A software suite for activated ion mobility mass spectrometry (aIM-MS) applied to multimeric protein assemblies , journal = International Journal of Mass Spectrometry , volume = 427 , pages = 20 - 28 , year = 2018 , note = Richard Smith Honor Issue , issn = 1387-3806 , doi = https://doi.org/10.1016/j.ijms.2017.08.014 , url = http://www.sciencedirect.com/science/article/pii/S1387380617302695 , author = Lukasz G. Migas and Aidan P. France and Bruno Bellina and Perdita E. Barran , keywords = Collision induced dissociation (CID), Collision induced unfolding (CIU), Activated ion mobility (aIM), Ion mobility (IM), Mass spectrometry (MS), Software, Python }","title":"BibTex"},{"location":"main/installation.html","text":"Installation Download You can download the latest version of ORIGAMI-ANALYSE from GitHub . Getting Started Actually, there is no actual installation! Simply copy the zipped folder onto your machine, unpack it and that's it! To start ORIGAMI-ANALYSE, double-click on the ORIGAMI.exe file. Requirements Requirements: Windows 7/8/10 HDD space: ~1 Gb Optional: Waters Driftscope (v2.7+)","title":"Installation"},{"location":"main/installation.html#installation","text":"","title":"Installation"},{"location":"main/installation.html#download","text":"You can download the latest version of ORIGAMI-ANALYSE from GitHub .","title":"Download"},{"location":"main/installation.html#getting-started","text":"Actually, there is no actual installation! Simply copy the zipped folder onto your machine, unpack it and that's it! To start ORIGAMI-ANALYSE, double-click on the ORIGAMI.exe file.","title":"Getting Started"},{"location":"main/installation.html#requirements","text":"Requirements: Windows 7/8/10 HDD space: ~1 Gb Optional: Waters Driftscope (v2.7+)","title":"Requirements"},{"location":"main/request.html","text":"Request New Features Go to the Google Forms If you would like me to add new features to ORIGAMI-ANALYSE, please use this form to do so. Do it right here Loading...","title":"Request New Features"},{"location":"main/request.html#request-new-features","text":"","title":"Request New Features"},{"location":"main/request.html#go-to-the-google-forms","text":"If you would like me to add new features to ORIGAMI-ANALYSE, please use this form to do so.","title":"Go to the Google Forms"},{"location":"main/request.html#do-it-right-here","text":"Loading...","title":"Do it right here"},{"location":"main/subscribe.html","text":"#mc_embed_signup{background:#fff; clear:left; font:14px Helvetica,Arial,sans-serif; } /<em> Add your own Mailchimp form style overrides in your site stylesheet or in this style block. We recommend moving this block and the preceding CSS link to the HEAD of your HTML file. </em>/ Subscribe to our mailing list indicates required Email Address First Name Last Name","title":"Newsletter"},{"location":"user-guide/example-files.html","text":"Example files Please feel free to download any of the examples files to get started. Automated CIU - Waters (.raw) An example file that was used in the original publication and can be used as training in analysis of ORIGAMI MS file format. Download file Manual DT-IMS - Waters (.raw) A set of files acquired over a number of drift voltages on our ancient DT-IMS instrument Download file Mass spectrum - text An example mass spectrum to get an idea of the file format. Download file - IDP Download file - mAb Heatmap - text A collection of three processed heatmaps that were presented in the original publication. These can be loaded, visualised and compared against each other in ORIGAMI ANALYSE . Download file Other data with metadata - text A collection of example fils that permit addition of visualisation metadata that can be useful when exporting data in an interactive format. Download file","title":"Example files"},{"location":"user-guide/example-files.html#example-files","text":"Please feel free to download any of the examples files to get started.","title":"Example files"},{"location":"user-guide/example-files.html#automated-ciu-waters-raw","text":"An example file that was used in the original publication and can be used as training in analysis of ORIGAMI MS file format. Download file","title":"Automated CIU - Waters (.raw)"},{"location":"user-guide/example-files.html#manual-dt-ims-waters-raw","text":"A set of files acquired over a number of drift voltages on our ancient DT-IMS instrument Download file","title":"Manual DT-IMS - Waters (.raw)"},{"location":"user-guide/example-files.html#mass-spectrum-text","text":"An example mass spectrum to get an idea of the file format. Download file - IDP Download file - mAb","title":"Mass spectrum - text"},{"location":"user-guide/example-files.html#heatmap-text","text":"A collection of three processed heatmaps that were presented in the original publication. These can be loaded, visualised and compared against each other in ORIGAMI ANALYSE . Download file","title":"Heatmap - text"},{"location":"user-guide/example-files.html#other-data-with-metadata-text","text":"A collection of example fils that permit addition of visualisation metadata that can be useful when exporting data in an interactive format. Download file","title":"Other data with metadata - text"},{"location":"user-guide/loading-data.html","text":"Loading data How to load data There are several different ways how you can load your data Use the file menu. File - Open... Use the toolbar. Click on any of the available buttons Use a keyboard shortcut: CTRL+SHIFT+P - open ORIGAMI project file CTRL+R - open Waters (.raw) file - IM-MS CTRL+C - open Waters (.raw) file - CCS calibration CTRL+F - open Waters (.raw) file - DT-IMS CTRL+T - open heatmap text (.csv/.txt/.tab) file CTRL+SHIFT+C - open multiple heatmap text (.csv/.txt/.tab) files CTRL+V - get mass spectrum from clipboard Load directly from data panels (Multiple files, DT-IMS, Text files) Drag-and-drop files in the window or into the panel Supported file formats Raw files: Waters (.raw) MS and IM-MS Community files: Mascot Generic Format (.mgf), identification mzML (mzIdentML) Text: .csv/.txt/.tab - MS, DT, RT, heatmap, data with metadata Clipboard: - MS data only Supported datasets MS IM-MS CIU (manual and ORIGAMI MS acquired) SID (manual) UVPD IRMPD DT-IMS - still at experimental stage CCS calibration - still at experimental stage","title":"Opening files"},{"location":"user-guide/loading-data.html#loading-data","text":"","title":"Loading data"},{"location":"user-guide/loading-data.html#how-to-load-data","text":"There are several different ways how you can load your data Use the file menu. File - Open... Use the toolbar. Click on any of the available buttons Use a keyboard shortcut: CTRL+SHIFT+P - open ORIGAMI project file CTRL+R - open Waters (.raw) file - IM-MS CTRL+C - open Waters (.raw) file - CCS calibration CTRL+F - open Waters (.raw) file - DT-IMS CTRL+T - open heatmap text (.csv/.txt/.tab) file CTRL+SHIFT+C - open multiple heatmap text (.csv/.txt/.tab) files CTRL+V - get mass spectrum from clipboard Load directly from data panels (Multiple files, DT-IMS, Text files) Drag-and-drop files in the window or into the panel","title":"How to load data"},{"location":"user-guide/loading-data.html#supported-file-formats","text":"Raw files: Waters (.raw) MS and IM-MS Community files: Mascot Generic Format (.mgf), identification mzML (mzIdentML) Text: .csv/.txt/.tab - MS, DT, RT, heatmap, data with metadata Clipboard: - MS data only","title":"Supported file formats"},{"location":"user-guide/loading-data.html#supported-datasets","text":"MS IM-MS CIU (manual and ORIGAMI MS acquired) SID (manual) UVPD IRMPD DT-IMS - still at experimental stage CCS calibration - still at experimental stage","title":"Supported datasets"},{"location":"user-guide/data-handling/automated-ciu.html","text":"Analysis of ORIGAMI-MS datasets In this example we will use file provided with the ORIGAMI distribution. You can download it here or it should be found in your ORIGAMI directory ( example_data/origami_ms ). Data loading Please have a look at MS and IM-MS data loading . Data extraction Please have a look at MS and IM-MS data extraction . ORIGAMI-MS method ORIGAMI-MS acquired files are simply CIU datasets that were acquired within a single file in which the collision voltage (or cone voltage) were ramped to increase the activation energy. There are four methods available which either increase or keep constant the number of scans-per-voltage as the energy increases. Linear: the collision voltage (CV) is ramped from Start Voltage (StartV) to End Voltage (EndV) with Step Voltage (StepV) as the increment. The number of scans-per-voltage stays the same and is controlled by Scans per Voltage (SPV) . Exponential: the CV is ramped from StartV to EndV with StepV as the increment. The SPVs increase as a function of an exponential function where the user specifies the Exponential % and Exponential Increment . These values determine the rate of the increase. Boltzmann: the CV is ramped from StartV to EndV with StepV as the increment. The SPVs increase as a function of an Boltzmann function where the user specifies the Boltzmann Offset . These values determine the rate of the increase. User-defined: values of SPV and CV are provided in a list by the user. The user-defined list looks something like this and is usually provided as a .csv file. SPV CV 3 5 6 10 9 12 12 20 Getting started The first thing to consider when analysing ORIGAMI-MS based files is the fact that they have a definitive start and end. These two points correspond to the initial and final collision voltage used during the acquisition. ORIGAMI-MS inserts two reporter regions into the acquisition window, and they tend to manifest itself as significant (or sometimes not) dips in the signal intensity. If you started the acquisition correctly, they should be easy to spot. See below for an example How to determine first scan Change the view to the RT (chromatogram) tab Zoom-in on the 'reporter' region in the retention time plot. The first value after the break is the start scan which will be used later on. In this case, the start scan is 7 which means the first CV in the experiment was applied on the 7th scan. How to determine ORIGAMI-MS parameters There are only two ways you can determine what parameters were used in the acquisition. You saved them in your labbook or in the header of the MassLynx file (recommended) You saved them to a .csv file using the Save parameters button in ORIGAMI-MS window during your acquisition If you have done neither of these things, you can try to figure out your parameters by going to the folder containing ORIGAMI-MS program and looking for the appropriate ORIGAMI_log_ DATE-TIME .log file which contains all commands executed by the program. How to combine the same CVs into one This is a crucial step that will combine multiple scans into one, corresponding to the typical CIU file. First, you must select ions of interest in the MS and subsequently extract the data. Once you've done that, follow these steps. ORIGAMI-MS panel Open the Processing panel ( SHIFT+2 keyboard shortcut or Menu - Process - Settings: ORIGAMI or click on the button) Fill-in all necessary parameters (depending on your acquisition method). In the example case, we've used: start scan - 7 , start voltage - 4 , final voltage - 200 , step voltage - 2.0 , scans-per-voltage - 3 . Go to the Panel: Peaklist and select some or all extracted ions In the toolbar, click on the Process( ) button and select - Combine collision voltages for selected/all ions (ORIGAMI) Ions with combined CVs should appear in the Document tree under Drift time (2D, combined voltages, EIC) . The toolbar - Process menu: Comparison of the all-ion, extracted-ion and combined voltage EIC heatmaps: Extracting mass spectra for each CV Once you've associated ORIGAMI-MS parameters with the opened file, you can extract mass spectrum for each CV. Provide ORIGAMI-MS parameters (same as above #1) In the toolbar, click on the Process( ) button and select Extract mass spectra for each collision voltage (ORIGAMI). If the check Bin mass spectra during extraction is selected, mass spectra will be automatically linearized based on the parameters set in the Processing panel: Mass spectrum . Extraction can take several seconds - minutes. All MS data will appear in your document under Mass Spectra All extracted mass spectra shown in a waterfall-like plot Processing heatmaps By default, all heatmaps will show the raw data which might not always be the most visually pleasing. In some circumstances, it might be necessary to process (e.g. normalize or smooth) the data. Panel processing: 2D Select any number of ions in the peaklist. In the toolbar, click on the Process( ) button and select - Process selected/all ions. Ions will be process based on the parameters in the Processing panel: 2D . All process data will appear in the document with the (processed) tag attached to the name. Comparison of processing of some processing methods.","title":"Automated CIU datasets (ORIGAMI<sup>MS</sup>)"},{"location":"user-guide/data-handling/automated-ciu.html#analysis-of-origami-ms-datasets","text":"In this example we will use file provided with the ORIGAMI distribution. You can download it here or it should be found in your ORIGAMI directory ( example_data/origami_ms ).","title":"Analysis of ORIGAMI-MS datasets"},{"location":"user-guide/data-handling/automated-ciu.html#data-loading","text":"Please have a look at MS and IM-MS data loading .","title":"Data loading"},{"location":"user-guide/data-handling/automated-ciu.html#data-extraction","text":"Please have a look at MS and IM-MS data extraction .","title":"Data extraction"},{"location":"user-guide/data-handling/automated-ciu.html#origami-ms-method","text":"ORIGAMI-MS acquired files are simply CIU datasets that were acquired within a single file in which the collision voltage (or cone voltage) were ramped to increase the activation energy. There are four methods available which either increase or keep constant the number of scans-per-voltage as the energy increases. Linear: the collision voltage (CV) is ramped from Start Voltage (StartV) to End Voltage (EndV) with Step Voltage (StepV) as the increment. The number of scans-per-voltage stays the same and is controlled by Scans per Voltage (SPV) . Exponential: the CV is ramped from StartV to EndV with StepV as the increment. The SPVs increase as a function of an exponential function where the user specifies the Exponential % and Exponential Increment . These values determine the rate of the increase. Boltzmann: the CV is ramped from StartV to EndV with StepV as the increment. The SPVs increase as a function of an Boltzmann function where the user specifies the Boltzmann Offset . These values determine the rate of the increase. User-defined: values of SPV and CV are provided in a list by the user. The user-defined list looks something like this and is usually provided as a .csv file. SPV CV 3 5 6 10 9 12 12 20","title":"ORIGAMI-MS method"},{"location":"user-guide/data-handling/automated-ciu.html#getting-started","text":"The first thing to consider when analysing ORIGAMI-MS based files is the fact that they have a definitive start and end. These two points correspond to the initial and final collision voltage used during the acquisition. ORIGAMI-MS inserts two reporter regions into the acquisition window, and they tend to manifest itself as significant (or sometimes not) dips in the signal intensity. If you started the acquisition correctly, they should be easy to spot. See below for an example","title":"Getting started"},{"location":"user-guide/data-handling/automated-ciu.html#how-to-determine-first-scan","text":"Change the view to the RT (chromatogram) tab Zoom-in on the 'reporter' region in the retention time plot. The first value after the break is the start scan which will be used later on. In this case, the start scan is 7 which means the first CV in the experiment was applied on the 7th scan.","title":"How to determine first scan"},{"location":"user-guide/data-handling/automated-ciu.html#how-to-determine-origami-ms-parameters","text":"There are only two ways you can determine what parameters were used in the acquisition. You saved them in your labbook or in the header of the MassLynx file (recommended) You saved them to a .csv file using the Save parameters button in ORIGAMI-MS window during your acquisition If you have done neither of these things, you can try to figure out your parameters by going to the folder containing ORIGAMI-MS program and looking for the appropriate ORIGAMI_log_ DATE-TIME .log file which contains all commands executed by the program.","title":"How to determine ORIGAMI-MS parameters"},{"location":"user-guide/data-handling/automated-ciu.html#how-to-combine-the-same-cvs-into-one","text":"This is a crucial step that will combine multiple scans into one, corresponding to the typical CIU file. First, you must select ions of interest in the MS and subsequently extract the data. Once you've done that, follow these steps. ORIGAMI-MS panel Open the Processing panel ( SHIFT+2 keyboard shortcut or Menu - Process - Settings: ORIGAMI or click on the button) Fill-in all necessary parameters (depending on your acquisition method). In the example case, we've used: start scan - 7 , start voltage - 4 , final voltage - 200 , step voltage - 2.0 , scans-per-voltage - 3 . Go to the Panel: Peaklist and select some or all extracted ions In the toolbar, click on the Process( ) button and select - Combine collision voltages for selected/all ions (ORIGAMI) Ions with combined CVs should appear in the Document tree under Drift time (2D, combined voltages, EIC) . The toolbar - Process menu: Comparison of the all-ion, extracted-ion and combined voltage EIC heatmaps:","title":"How to combine the same CVs into one"},{"location":"user-guide/data-handling/automated-ciu.html#extracting-mass-spectra-for-each-cv","text":"Once you've associated ORIGAMI-MS parameters with the opened file, you can extract mass spectrum for each CV. Provide ORIGAMI-MS parameters (same as above #1) In the toolbar, click on the Process( ) button and select Extract mass spectra for each collision voltage (ORIGAMI). If the check Bin mass spectra during extraction is selected, mass spectra will be automatically linearized based on the parameters set in the Processing panel: Mass spectrum . Extraction can take several seconds - minutes. All MS data will appear in your document under Mass Spectra All extracted mass spectra shown in a waterfall-like plot","title":"Extracting mass spectra for each CV"},{"location":"user-guide/data-handling/automated-ciu.html#processing-heatmaps","text":"By default, all heatmaps will show the raw data which might not always be the most visually pleasing. In some circumstances, it might be necessary to process (e.g. normalize or smooth) the data. Panel processing: 2D Select any number of ions in the peaklist. In the toolbar, click on the Process( ) button and select - Process selected/all ions. Ions will be process based on the parameters in the Processing panel: 2D . All process data will appear in the document with the (processed) tag attached to the name. Comparison of processing of some processing methods.","title":"Processing heatmaps"},{"location":"user-guide/data-handling/manual-ciu.html","text":"Analysis of manual CIU/SID/multi-field DTIMS datasets In this example we will use files provided with the ORIGAMI distribution. You can download them here or it should be found in your ORIGAMI directory ( example_data/multi-field-dtims ). Manual CIU/SID/multi-field DTIMS Manual CIU/SID/DTIMS datasets consist of multiple files, each differing usually in the energy introduced to the system to either induce fragmentation or unfolding. In our case, we will be using CIU dataset where the collision energy was raised by several volts and we can observe some levels of unfolding. Data loading To load multiple Waters (.raw) files, please use any of the following: Use the file menu. File - Open multiple MassLynx (.raw) files [CIU] Use the toolbar. Click on the button Use a keyboard shortcut: CTRL+SHIFT-R - open multiple Waters (.raw) files - IM-MS Drag-and-drop files in the Multiple files panel When you have added files to ORIGAMI-ANALYSE, you will be asked to provide document name and document path. If you would like to add more files to the same document, make sure you click on the document in the Document tree and then use any of the above options to load data. Manual CIU document ORIGAMI-ANALYSE utilises documents to maintain all raw and processed data. The MANUAL document is a little different, as it requires different type of processing as it is pooling results from multiple files into one. When data is loaded, ORIGAMI-ANALYSE will only load the mass spectra and all-ion mobility data. In addition, a average mass spectrum will be generated from all spectra loaded in. This spectrum will be available under the Mass Spectrum tag in the document tree whereas individual spectra will be shown under the Mass Spectra sub-tree. Data extraction Although we are dealing with multiple files simulatenously now, data extraction is no different. Please have a look at MS and IM-MS data extraction . In short, you press-and-hold CTRL on your keyboard and drag with your mouse (while holding left-button) in the mass spectrum. An ion is added to the Panel: Peaklist from where you can extract its information. Stitching-up several files together When data is being extracted for specific ion, ORIGAMI-ANALYSE will use the 'variable' column in the Panel: Multiple files to determine the order in which files should be added. This column can be numerical (e.g. collision voltage, drift voltage) or alphabetical (e.g. name). If no value is provided, its not going to be pretty... Getting started The example provided is a set of files from a linear drift-tube experiment where each file corresponds to different drift voltage. So the variable that will be set in the table is the drift voltage and in this case, is written in the file name. When you have added these files to ORIGAMI-ANALYSE, you will be asked to specify document name and document path. In this case, yu can simply call it moqtof (name of the instrument it was acquired on). There are 6 files with drift voltages of 20, 25, 30, 35, 45, 50 and 60 V. As you will notice, when these files were added, the value of variable is set to 0, as the DV parameter is not saved in the MassLynx (.raw) file. You can specify by double-clicking in the variable column and typing appropriate value. Clicking on any column header will automatically sort the table. Panel: Multiple-files Combining data from multiple files into one Once you have added ions to the peaklist, you can extract that information . Changing x/y-axis labels By default, the label associated with combined dataset is 'Collision Voltage (V)' as it is expect to be a CIU-like dataset. In our case it is drift voltage, so once the ions have been combined, we can change the label in the Document Tree. Average mass spectrum The average mass spectrum generated when the data is being added to the document might not have the desired parameters. You can 're-average' the mass spectra by selecting relevant items int the filelist and then clicking on the Process... button and selecting Average mass spectra (current document) . ORIGAMI-ANALYSE will use the parameters set in the Processing panel: Mass Spectrum . Plotting and replotting The easiest way to plot anything in ORIGAMI-ANALYSE is to do it from the Document Tree and either double-clicking on the desired item or right-clicking and selecting appropriate option. Alternatively, you can right-click on an item in the Panel: Multiple-files and select either Show mass spectrum or Show mobiligram . Customising item Some parameters, such as variable or label can be changed by double-clicking in the appropriate field in the table and typing-in a value. Others, such as color can only be changed by right-clicking and selecint Assign new color . You also do this in batch by selecting several items in the list and clicking on the Annotate... button.","title":"Manual CIU/SID datasets"},{"location":"user-guide/data-handling/manual-ciu.html#analysis-of-manual-ciusidmulti-field-dtims-datasets","text":"In this example we will use files provided with the ORIGAMI distribution. You can download them here or it should be found in your ORIGAMI directory ( example_data/multi-field-dtims ).","title":"Analysis of manual CIU/SID/multi-field DTIMS datasets"},{"location":"user-guide/data-handling/manual-ciu.html#manual-ciusidmulti-field-dtims","text":"Manual CIU/SID/DTIMS datasets consist of multiple files, each differing usually in the energy introduced to the system to either induce fragmentation or unfolding. In our case, we will be using CIU dataset where the collision energy was raised by several volts and we can observe some levels of unfolding.","title":"Manual CIU/SID/multi-field DTIMS"},{"location":"user-guide/data-handling/manual-ciu.html#data-loading","text":"To load multiple Waters (.raw) files, please use any of the following: Use the file menu. File - Open multiple MassLynx (.raw) files [CIU] Use the toolbar. Click on the button Use a keyboard shortcut: CTRL+SHIFT-R - open multiple Waters (.raw) files - IM-MS Drag-and-drop files in the Multiple files panel When you have added files to ORIGAMI-ANALYSE, you will be asked to provide document name and document path. If you would like to add more files to the same document, make sure you click on the document in the Document tree and then use any of the above options to load data.","title":"Data loading"},{"location":"user-guide/data-handling/manual-ciu.html#manual-ciu-document","text":"ORIGAMI-ANALYSE utilises documents to maintain all raw and processed data. The MANUAL document is a little different, as it requires different type of processing as it is pooling results from multiple files into one. When data is loaded, ORIGAMI-ANALYSE will only load the mass spectra and all-ion mobility data. In addition, a average mass spectrum will be generated from all spectra loaded in. This spectrum will be available under the Mass Spectrum tag in the document tree whereas individual spectra will be shown under the Mass Spectra sub-tree.","title":"Manual CIU document"},{"location":"user-guide/data-handling/manual-ciu.html#data-extraction","text":"Although we are dealing with multiple files simulatenously now, data extraction is no different. Please have a look at MS and IM-MS data extraction . In short, you press-and-hold CTRL on your keyboard and drag with your mouse (while holding left-button) in the mass spectrum. An ion is added to the Panel: Peaklist from where you can extract its information.","title":"Data extraction"},{"location":"user-guide/data-handling/manual-ciu.html#stitching-up-several-files-together","text":"When data is being extracted for specific ion, ORIGAMI-ANALYSE will use the 'variable' column in the Panel: Multiple files to determine the order in which files should be added. This column can be numerical (e.g. collision voltage, drift voltage) or alphabetical (e.g. name). If no value is provided, its not going to be pretty...","title":"Stitching-up several files together"},{"location":"user-guide/data-handling/manual-ciu.html#getting-started","text":"The example provided is a set of files from a linear drift-tube experiment where each file corresponds to different drift voltage. So the variable that will be set in the table is the drift voltage and in this case, is written in the file name. When you have added these files to ORIGAMI-ANALYSE, you will be asked to specify document name and document path. In this case, yu can simply call it moqtof (name of the instrument it was acquired on). There are 6 files with drift voltages of 20, 25, 30, 35, 45, 50 and 60 V. As you will notice, when these files were added, the value of variable is set to 0, as the DV parameter is not saved in the MassLynx (.raw) file. You can specify by double-clicking in the variable column and typing appropriate value. Clicking on any column header will automatically sort the table. Panel: Multiple-files","title":"Getting started"},{"location":"user-guide/data-handling/manual-ciu.html#combining-data-from-multiple-files-into-one","text":"Once you have added ions to the peaklist, you can extract that information .","title":"Combining data from multiple files into one"},{"location":"user-guide/data-handling/manual-ciu.html#changing-xy-axis-labels","text":"By default, the label associated with combined dataset is 'Collision Voltage (V)' as it is expect to be a CIU-like dataset. In our case it is drift voltage, so once the ions have been combined, we can change the label in the Document Tree.","title":"Changing x/y-axis labels"},{"location":"user-guide/data-handling/manual-ciu.html#average-mass-spectrum","text":"The average mass spectrum generated when the data is being added to the document might not have the desired parameters. You can 're-average' the mass spectra by selecting relevant items int the filelist and then clicking on the Process... button and selecting Average mass spectra (current document) . ORIGAMI-ANALYSE will use the parameters set in the Processing panel: Mass Spectrum .","title":"Average mass spectrum"},{"location":"user-guide/data-handling/manual-ciu.html#plotting-and-replotting","text":"The easiest way to plot anything in ORIGAMI-ANALYSE is to do it from the Document Tree and either double-clicking on the desired item or right-clicking and selecting appropriate option. Alternatively, you can right-click on an item in the Panel: Multiple-files and select either Show mass spectrum or Show mobiligram .","title":"Plotting and replotting"},{"location":"user-guide/data-handling/manual-ciu.html#customising-item","text":"Some parameters, such as variable or label can be changed by double-clicking in the appropriate field in the table and typing-in a value. Others, such as color can only be changed by right-clicking and selecint Assign new color . You also do this in batch by selecting several items in the list and clicking on the Annotate... button.","title":"Customising item"},{"location":"user-guide/data-handling/ms-and-imms-files.html","text":"Analysis of MS and IM-MS files In this example, we will use a file provided in the example. You can download it from here or it should be found in your ORIGAMI directory ( example_data/origami_ms ). Video tutorial of how to load and process Waters (.raw) files Data loading To load Waters (.raw) files, please use any of the following: Use the file menu. File - Open ORIGAMI MassLynx (.raw) file [CIU] Use the toolbar. Click on the button Use a keyboard shortcut: CTRL+R - open Waters (.raw) file - IM-MS Drag-and-drop the file in the main window Document tree Any file you open will result in generation of a ORIGAMI document that will contain all data that you will generate. It is structured just like a directory on your PC so it should be easy to get used to. When you right-click on any item, a custom menu will appear from which you can figure out what you would like to do. An example is shown below: Plotting and replotting You can either double-click on an item in the Document tree or right-click and select the option \"Show...\". If you would like to clear a plot, right-click in the plot area and select \"Clear plot\". Data extraction You can extract various types of data from Waters (.raw) files. The type you extract will depend on the window you are currently viewing. So, if you are in the MS window, you can extract heatmap , mobility and chromatography data. If you are in the RT , 1D or 2D windows, you can extract mass spectra . To select region you would like to extract, press and hold CTRL on your keyboard and left-click drag your mouse on the selected region. Most data will be automatically extracted (except for heatmaps - will discuss shortly). Data that has been extracted will be automatically added to your document . Mass spectra (from RT, 1D, 2D windows) The extracted mass spectra can either represent the raw data or linearized data, depending on what settings you have enabled. To change this behaviour, open the Processing window , go to Mass spectrum and check (or uncheck) the \"Enable MS linearization in chromatogram/mobiligram window\". You can also change linearization settings in this panel. If you are extracting from the RT window, chromatographic information will be used, from the 1D window, drift time and from 2D window, both will be used. Extracted data will appear under Mass Spectra . Video tutorial of how to extract mass spectra from Waters (.raw) files Heatmaps (from MS window) When you extract data from the MS window, an ion will automatically be added to the Peaklist. This panel serves as main select-and-compare tool for easy visualisation of multiple items together. In order for the data to be extracted, you must click on the button and a new menu will appear where appear where you can select the \"Extract all ions\". If, in future you would like to automatically extract heatmaps, click on the \"Extract automatically\" toggle. Extracted data will appear under Drift time (2D, EIC) . Chromatograms (from DT/MS window) You can extract chromatograms in the DT/MS window where the m/z and drift time information will be taken into account during data extraction. Extracted data will appear under Chromatograms (EIC) . Panel: Peaklist All heatmaps are automatically added to the Panel peaklist which usually appears on the right-hand side of the window. From here, you can easily visualise, customise and compare data. When you right-click on any item in the list, a menu will appear from which you can easily access various visualisation modes and customisation settings. When you double-click on an item (or right-click and select \"Edit file information\") a new window will appear where you can change certain parameters, such as ORIGAMI MS parameters, charge state, color, colormap, etc . Processing mass spectra Mass spectra imported using Driftscope are automatically normalized to 1 (not my fault, I promise!). Sometimes, it might be necessary to remove noise or smooth the spectrum so it is more visually appealing. Panel processing: MS Right-click on any mass spectrum in the Document tree (e.g. Mass Spectrum) and select Process... . A new window will appear where you can adjust processing parameters. Click on the Replot button if you first want to see how the data will look or Process if you would like to add that data to the document. Processing heatmaps By default, all heatmaps will show the raw data which might not always be the most visually pleasing. In some circumstances, it might be necessary to process (e.g. normalize or smooth) the data. Panel processing: 2D Depending what are you planning on processing (e.g. extracted ion heatmap or whole-file heatmap), you can perform processing in the Panel: Peaklist or in the Document tree . Processing from Panel: Peaklist Select any number of ions in the peaklist. In the toolbar, click on the Process( ) button and select - Process selected/all ions. Ions will be process based on the parameters in the Processing panel: 2D . All process data will appear in the document with the (processed) tag attached to the name. Processing from Document tree Right-click on a desired item in the Document tree (e.g. Drift time (2D)) and select Process... A new window will appear where you can adjust processing parameters Click on the Replot button if you first want to see how the data will look or Process if you would like to add that data to the document. Comparison of processing of some of the processing methods","title":"MS and IM-MS files"},{"location":"user-guide/data-handling/ms-and-imms-files.html#analysis-of-ms-and-im-ms-files","text":"In this example, we will use a file provided in the example. You can download it from here or it should be found in your ORIGAMI directory ( example_data/origami_ms ).","title":"Analysis of MS and IM-MS files"},{"location":"user-guide/data-handling/ms-and-imms-files.html#video-tutorial-of-how-to-load-and-process-waters-raw-files","text":"","title":"Video tutorial of how to load and process Waters (.raw) files"},{"location":"user-guide/data-handling/ms-and-imms-files.html#data-loading","text":"To load Waters (.raw) files, please use any of the following: Use the file menu. File - Open ORIGAMI MassLynx (.raw) file [CIU] Use the toolbar. Click on the button Use a keyboard shortcut: CTRL+R - open Waters (.raw) file - IM-MS Drag-and-drop the file in the main window","title":"Data loading"},{"location":"user-guide/data-handling/ms-and-imms-files.html#document-tree","text":"Any file you open will result in generation of a ORIGAMI document that will contain all data that you will generate. It is structured just like a directory on your PC so it should be easy to get used to. When you right-click on any item, a custom menu will appear from which you can figure out what you would like to do. An example is shown below:","title":"Document tree"},{"location":"user-guide/data-handling/ms-and-imms-files.html#plotting-and-replotting","text":"You can either double-click on an item in the Document tree or right-click and select the option \"Show...\". If you would like to clear a plot, right-click in the plot area and select \"Clear plot\".","title":"Plotting and replotting"},{"location":"user-guide/data-handling/ms-and-imms-files.html#data-extraction","text":"You can extract various types of data from Waters (.raw) files. The type you extract will depend on the window you are currently viewing. So, if you are in the MS window, you can extract heatmap , mobility and chromatography data. If you are in the RT , 1D or 2D windows, you can extract mass spectra . To select region you would like to extract, press and hold CTRL on your keyboard and left-click drag your mouse on the selected region. Most data will be automatically extracted (except for heatmaps - will discuss shortly). Data that has been extracted will be automatically added to your document .","title":"Data extraction"},{"location":"user-guide/data-handling/ms-and-imms-files.html#mass-spectra-from-rt-1d-2d-windows","text":"The extracted mass spectra can either represent the raw data or linearized data, depending on what settings you have enabled. To change this behaviour, open the Processing window , go to Mass spectrum and check (or uncheck) the \"Enable MS linearization in chromatogram/mobiligram window\". You can also change linearization settings in this panel. If you are extracting from the RT window, chromatographic information will be used, from the 1D window, drift time and from 2D window, both will be used. Extracted data will appear under Mass Spectra .","title":"Mass spectra (from RT, 1D, 2D windows)"},{"location":"user-guide/data-handling/ms-and-imms-files.html#video-tutorial-of-how-to-extract-mass-spectra-from-waters-raw-files","text":"","title":"Video tutorial of how to extract mass spectra from Waters (.raw) files"},{"location":"user-guide/data-handling/ms-and-imms-files.html#heatmaps-from-ms-window","text":"When you extract data from the MS window, an ion will automatically be added to the Peaklist. This panel serves as main select-and-compare tool for easy visualisation of multiple items together. In order for the data to be extracted, you must click on the button and a new menu will appear where appear where you can select the \"Extract all ions\". If, in future you would like to automatically extract heatmaps, click on the \"Extract automatically\" toggle. Extracted data will appear under Drift time (2D, EIC) .","title":"Heatmaps (from MS window)"},{"location":"user-guide/data-handling/ms-and-imms-files.html#chromatograms-from-dtms-window","text":"You can extract chromatograms in the DT/MS window where the m/z and drift time information will be taken into account during data extraction. Extracted data will appear under Chromatograms (EIC) .","title":"Chromatograms (from DT/MS window)"},{"location":"user-guide/data-handling/ms-and-imms-files.html#panel-peaklist","text":"All heatmaps are automatically added to the Panel peaklist which usually appears on the right-hand side of the window. From here, you can easily visualise, customise and compare data. When you right-click on any item in the list, a menu will appear from which you can easily access various visualisation modes and customisation settings. When you double-click on an item (or right-click and select \"Edit file information\") a new window will appear where you can change certain parameters, such as ORIGAMI MS parameters, charge state, color, colormap, etc .","title":"Panel: Peaklist"},{"location":"user-guide/data-handling/ms-and-imms-files.html#processing-mass-spectra","text":"Mass spectra imported using Driftscope are automatically normalized to 1 (not my fault, I promise!). Sometimes, it might be necessary to remove noise or smooth the spectrum so it is more visually appealing.","title":"Processing mass spectra"},{"location":"user-guide/data-handling/ms-and-imms-files.html#panel-processing-ms","text":"Right-click on any mass spectrum in the Document tree (e.g. Mass Spectrum) and select Process... . A new window will appear where you can adjust processing parameters. Click on the Replot button if you first want to see how the data will look or Process if you would like to add that data to the document.","title":"Panel processing: MS"},{"location":"user-guide/data-handling/ms-and-imms-files.html#processing-heatmaps","text":"By default, all heatmaps will show the raw data which might not always be the most visually pleasing. In some circumstances, it might be necessary to process (e.g. normalize or smooth) the data.","title":"Processing heatmaps"},{"location":"user-guide/data-handling/ms-and-imms-files.html#panel-processing-2d","text":"Depending what are you planning on processing (e.g. extracted ion heatmap or whole-file heatmap), you can perform processing in the Panel: Peaklist or in the Document tree .","title":"Panel processing: 2D"},{"location":"user-guide/data-handling/ms-and-imms-files.html#processing-from-panel-peaklist","text":"Select any number of ions in the peaklist. In the toolbar, click on the Process( ) button and select - Process selected/all ions. Ions will be process based on the parameters in the Processing panel: 2D . All process data will appear in the document with the (processed) tag attached to the name.","title":"Processing from Panel: Peaklist"},{"location":"user-guide/data-handling/ms-and-imms-files.html#processing-from-document-tree","text":"Right-click on a desired item in the Document tree (e.g. Drift time (2D)) and select Process... A new window will appear where you can adjust processing parameters Click on the Replot button if you first want to see how the data will look or Process if you would like to add that data to the document.","title":"Processing from Document tree"},{"location":"user-guide/data-handling/ms-and-imms-files.html#comparison-of-processing-of-some-of-the-processing-methods","text":"","title":"Comparison of processing of some of the processing methods"},{"location":"user-guide/data-handling/text-files.html","text":"Analysis of text files In this example we will use files provided with the ORIGAMI distribution. You can download MS file and heatmap file or you can find them in your ORIGAMI directory ( example_data/text ). Data loading To load text files, please use any of the following: Use the file menu. File - Open IM-MS Text file [CIU] or Open MS Text file Use the toolbar. Click on the T or T+ button Use a keyboard shortcut: CTRL+T - open heatmap text (.csv/.txt/.tab) file Drag-and-drop the file in the main window Clipboard: - MS data only Document tree Any file you open will result in generation of a ORIGAMI document that will contain all data that you will generate. It is structured just like a directory on your PC so it should be easy to get used to. When you right-click on any item, a custom menu will appear from which you can figure out what you would like to do. An example is shown below: Plotting and replotting You can either double-click on an item in the Document tree or right-click and select the option \"Show...\". If you would like to clear a plot, right-click in the plot area and select \"Clear plot\". Panel: Textlist All text-based heatmaps are automatically added to the Panel textlist which usually appears on the right-hand side of the window. From here, you can easily visualise, customise and compare data. When you right-click on any item in the list, a menu will appear from which you can easily access various visualisation modes and customisation settings. When you double-click on an item (or right-click and select \"Edit file information\") a new window will appear where you can change certain parameters, such as charge state, color, colormap, etc . Processing heatmaps By default, all heatmaps will show the raw data which might not always be the most visually pleasing. In some circumstances, it might be necessary to process (e.g. normalize or smooth) the data. Processing panel: 2D Processing from Panel: Textlist Select any number of ions in the textlist. In the toolbar, click on the Process( ) button and select - Process selected/all ions. Ions will be process based on the parameters in the Processing panel: 2D . All process data will appear in the document with the (processed) tag attached to the name. Processing from Document tree Right-click on a desired item in the Document tree (e.g. Drift time (2D)) and select Process... A new window will appear where you can adjust processing parameters Click on the Replot button if you first want to see how the data will look or Process if you would like to add that data to the document.","title":"Text files"},{"location":"user-guide/data-handling/text-files.html#analysis-of-text-files","text":"In this example we will use files provided with the ORIGAMI distribution. You can download MS file and heatmap file or you can find them in your ORIGAMI directory ( example_data/text ).","title":"Analysis of text files"},{"location":"user-guide/data-handling/text-files.html#data-loading","text":"To load text files, please use any of the following: Use the file menu. File - Open IM-MS Text file [CIU] or Open MS Text file Use the toolbar. Click on the T or T+ button Use a keyboard shortcut: CTRL+T - open heatmap text (.csv/.txt/.tab) file Drag-and-drop the file in the main window Clipboard: - MS data only","title":"Data loading"},{"location":"user-guide/data-handling/text-files.html#document-tree","text":"Any file you open will result in generation of a ORIGAMI document that will contain all data that you will generate. It is structured just like a directory on your PC so it should be easy to get used to. When you right-click on any item, a custom menu will appear from which you can figure out what you would like to do. An example is shown below:","title":"Document tree"},{"location":"user-guide/data-handling/text-files.html#plotting-and-replotting","text":"You can either double-click on an item in the Document tree or right-click and select the option \"Show...\". If you would like to clear a plot, right-click in the plot area and select \"Clear plot\".","title":"Plotting and replotting"},{"location":"user-guide/data-handling/text-files.html#panel-textlist","text":"All text-based heatmaps are automatically added to the Panel textlist which usually appears on the right-hand side of the window. From here, you can easily visualise, customise and compare data. When you right-click on any item in the list, a menu will appear from which you can easily access various visualisation modes and customisation settings. When you double-click on an item (or right-click and select \"Edit file information\") a new window will appear where you can change certain parameters, such as charge state, color, colormap, etc .","title":"Panel: Textlist"},{"location":"user-guide/data-handling/text-files.html#processing-heatmaps","text":"By default, all heatmaps will show the raw data which might not always be the most visually pleasing. In some circumstances, it might be necessary to process (e.g. normalize or smooth) the data.","title":"Processing heatmaps"},{"location":"user-guide/data-handling/text-files.html#processing-panel-2d","text":"","title":"Processing panel: 2D"},{"location":"user-guide/data-handling/text-files.html#processing-from-panel-textlist","text":"Select any number of ions in the textlist. In the toolbar, click on the Process( ) button and select - Process selected/all ions. Ions will be process based on the parameters in the Processing panel: 2D . All process data will appear in the document with the (processed) tag attached to the name.","title":"Processing from Panel: Textlist"},{"location":"user-guide/data-handling/text-files.html#processing-from-document-tree","text":"Right-click on a desired item in the Document tree (e.g. Drift time (2D)) and select Process... A new window will appear where you can adjust processing parameters Click on the Replot button if you first want to see how the data will look or Process if you would like to add that data to the document.","title":"Processing from Document tree"},{"location":"user-guide/deconvolution/unidec-change-window-view.html","text":"Changing UniDec window Since version 1.2.0.3, ORIGAMI-ANALYSE shows UniDec plots in a seperate tab rather than in the continous view. It is quite straightforward to switch back to the continous view . Open the Processing panel: UniDec ( SHIFT+6 on your keyboard or menu - Process - UniDec). Click on the Customise plots... button Change the setting: Panel view to what you would prefer. Note: This will only take effect when you restart ORIGAMI-ANALYSE.","title":"UniDec - changing window view "},{"location":"user-guide/deconvolution/unidec-change-window-view.html#changing-unidec-window","text":"Since version 1.2.0.3, ORIGAMI-ANALYSE shows UniDec plots in a seperate tab rather than in the continous view. It is quite straightforward to switch back to the continous view . Open the Processing panel: UniDec ( SHIFT+6 on your keyboard or menu - Process - UniDec). Click on the Customise plots... button Change the setting: Panel view to what you would prefer. Note: This will only take effect when you restart ORIGAMI-ANALYSE.","title":"Changing UniDec window"},{"location":"user-guide/deconvolution/unidec-customise-plots.html","text":"Customising UniDec plots In the case of UniDec plots, several parameters such as color schemes , marker size , heatmap parameters and others can be adjusted by opening the Processing panel: UniDec and then the Customisation panel . Open the Processing panel: UniDec ( SHIFT+6 on your keyboard or menu - Process - UniDec). Click on the Customise plots... button As you can see, most parameters have been split based on which plot they are applied to. You can simply change the parameter value, close the window and then replot the plot you want to improve (settings are not applied automatically). Settings such as line widths, line styles, figure size or label size can be adjusted through the Plot Editor panel that is accessible through (Menu - Plot settings or the toolbar icons )","title":"UniDec - customising plots "},{"location":"user-guide/deconvolution/unidec-customise-plots.html#customising-unidec-plots","text":"In the case of UniDec plots, several parameters such as color schemes , marker size , heatmap parameters and others can be adjusted by opening the Processing panel: UniDec and then the Customisation panel . Open the Processing panel: UniDec ( SHIFT+6 on your keyboard or menu - Process - UniDec). Click on the Customise plots... button As you can see, most parameters have been split based on which plot they are applied to. You can simply change the parameter value, close the window and then replot the plot you want to improve (settings are not applied automatically). Settings such as line widths, line styles, figure size or label size can be adjusted through the Plot Editor panel that is accessible through (Menu - Plot settings or the toolbar icons )","title":"Customising UniDec plots"},{"location":"user-guide/deconvolution/unidec-deconvolution.html","text":"UniDec deconvolution UniDec is a Bayesian deconvolution algorithm that can be used to deconvolute mass spectra and ion mobility-mass spectra. It was developed by Dr. Michael Marty and is freely available under the modified BSD licence. I would highly recommend you check-out UniDec (and MetaUniDec) software. If you use it in your work, please cite their work: M. T. Marty, A. J. Baldwin, E. G. Marklund, G. K. A. Hochberg, J. L. P. Benesch, C. V. Robinson, Anal. Chem. 2015, 87, 4370-4376. Video tutorial Deconvolution in ORIGAMI-ANALYSE Any mass spectrum within a ORIGAMI document can be deconvoluted and therefore a document can contain tens of spectra, each with its own deconvolution results. The easiest way to get started is to find an item in the Document Tree, right-click on it and select Deconvolute using UniDec... which will open a new panel where you can adjust the parameters. Example data In this example we will use a file provided with the ORIGAMI distribution. You can download MS file or you can find it in your ORIGAMI directory ( example_data/text ). This file contains a mass spectrum of a intrinsically disordered protein, p27 that is approx. 22.5 kDa in size and has a very broad charge state distribution. Loading data Please have a look at Loading Text files . In short, you either drag-and-drop the text file in the main window of ORIGAMI-ANALYSE or go to File - Open MS Text file . Deconvolution Once you've loaded data, right-click on it in the Document Tree and select Deconvolute using UniDec... If you are using the example file, you can start with the settings shown below: Specify Pre-processing parameters. You can start with m/z start = 500 and m/z end = 2500 with m/z bin size = 0.1 using Linear interpolation method. Click on the Pre-process button. If you are using the Tabbed view , the results will be shown in the tab UniDec - MS Specify deconvolution parameters. If you are unsure about the sample you are analysing, specify a broad range of charge states and the molecular weight with large-ish Sampling frequency. This will help you narrow down the appropriate range for your sample. Once you are happy, click on the Run UniDec button. If you are using the Tabbed view , the results will be shown in UniDec - m/z vs Charge / MW vs Charge / MW tabs. Following successful deconvolution, you can find peaks and identify the found molecular weights. To do this, specify appropriate parameters in the Peak detection parameters section and then click on the Detect peaks button. If you are using the Tabbed view , the results will be shown in UniDec - Isolated MS / Barplot tabs. Visualisation of results Visualisation of individual species If you are lucky, deconvolution will result in a single species being detect. This is rather unlikely and therefore you will be presented with a range of detected MW. In order to select and visualise only one species at at time, you can select an item with a molecular weight in the Dropdown menu (see below) and click on the Isolate button. You can also label its charge states by clicking on the Label button. Note: It is likely that the automatic label optimiser is enabled and you can change that by clicking on the Customise plots... button and unchecking the Optimise label position option. Saving plots The easiest way to save any plot in ORIGAMI-ANALYSE is to plot it, customise it and then right-click in the plot area and select Save figure... . Note: It is likely that the figure will be automatically resized to a pre-defined image size. This can very occasionally cause problems, therefore you disable that option by unchecking the Resize on saving menu item. Saving data All deconvolution data is saved within the document and if you to the Document Tree and open-up the item (see below), you can right-click on any item and select the option Save results . If you click on the UniDec header, you can save all results at the same time. Plotting and replotting Find the desired item in the Document Tree and double-click on it to plot it.","title":"UniDec - deconvolution"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#unidec-deconvolution","text":"UniDec is a Bayesian deconvolution algorithm that can be used to deconvolute mass spectra and ion mobility-mass spectra. It was developed by Dr. Michael Marty and is freely available under the modified BSD licence. I would highly recommend you check-out UniDec (and MetaUniDec) software. If you use it in your work, please cite their work: M. T. Marty, A. J. Baldwin, E. G. Marklund, G. K. A. Hochberg, J. L. P. Benesch, C. V. Robinson, Anal. Chem. 2015, 87, 4370-4376.","title":"UniDec deconvolution"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#video-tutorial","text":"","title":"Video tutorial"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#deconvolution-in-origami-analyse","text":"Any mass spectrum within a ORIGAMI document can be deconvoluted and therefore a document can contain tens of spectra, each with its own deconvolution results. The easiest way to get started is to find an item in the Document Tree, right-click on it and select Deconvolute using UniDec... which will open a new panel where you can adjust the parameters.","title":"Deconvolution in ORIGAMI-ANALYSE"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#example-data","text":"In this example we will use a file provided with the ORIGAMI distribution. You can download MS file or you can find it in your ORIGAMI directory ( example_data/text ). This file contains a mass spectrum of a intrinsically disordered protein, p27 that is approx. 22.5 kDa in size and has a very broad charge state distribution.","title":"Example data"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#loading-data","text":"Please have a look at Loading Text files . In short, you either drag-and-drop the text file in the main window of ORIGAMI-ANALYSE or go to File - Open MS Text file .","title":"Loading data"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#deconvolution","text":"Once you've loaded data, right-click on it in the Document Tree and select Deconvolute using UniDec... If you are using the example file, you can start with the settings shown below: Specify Pre-processing parameters. You can start with m/z start = 500 and m/z end = 2500 with m/z bin size = 0.1 using Linear interpolation method. Click on the Pre-process button. If you are using the Tabbed view , the results will be shown in the tab UniDec - MS Specify deconvolution parameters. If you are unsure about the sample you are analysing, specify a broad range of charge states and the molecular weight with large-ish Sampling frequency. This will help you narrow down the appropriate range for your sample. Once you are happy, click on the Run UniDec button. If you are using the Tabbed view , the results will be shown in UniDec - m/z vs Charge / MW vs Charge / MW tabs. Following successful deconvolution, you can find peaks and identify the found molecular weights. To do this, specify appropriate parameters in the Peak detection parameters section and then click on the Detect peaks button. If you are using the Tabbed view , the results will be shown in UniDec - Isolated MS / Barplot tabs.","title":"Deconvolution"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#visualisation-of-results","text":"","title":"Visualisation of results"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#visualisation-of-individual-species","text":"If you are lucky, deconvolution will result in a single species being detect. This is rather unlikely and therefore you will be presented with a range of detected MW. In order to select and visualise only one species at at time, you can select an item with a molecular weight in the Dropdown menu (see below) and click on the Isolate button. You can also label its charge states by clicking on the Label button. Note: It is likely that the automatic label optimiser is enabled and you can change that by clicking on the Customise plots... button and unchecking the Optimise label position option.","title":"Visualisation of individual species"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#saving-plots","text":"The easiest way to save any plot in ORIGAMI-ANALYSE is to plot it, customise it and then right-click in the plot area and select Save figure... . Note: It is likely that the figure will be automatically resized to a pre-defined image size. This can very occasionally cause problems, therefore you disable that option by unchecking the Resize on saving menu item.","title":"Saving plots"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#saving-data","text":"All deconvolution data is saved within the document and if you to the Document Tree and open-up the item (see below), you can right-click on any item and select the option Save results . If you click on the UniDec header, you can save all results at the same time.","title":"Saving data"},{"location":"user-guide/deconvolution/unidec-deconvolution.html#plotting-and-replotting","text":"Find the desired item in the Document Tree and double-click on it to plot it.","title":"Plotting and replotting"},{"location":"user-guide/interactive-output/simple-output.html","text":"Exporting interactive figures ORIGAMI enables creation of HTML/JavaScript webpages which embed interactive versions of figures visualised in ORIGAMI. Practically all figures that you can generate in the desktop application can be also exported to a HTML document that can be shared with your supervisor, journal reviewers or collaborators for their in-depth interrogation. While this might seem like a bit of a gimmick, it makes sense to share the results with the scientific community in a manner more explorative than a simple static image. See here for some helpful encouragement ( Perkel and Weissgerber ). Example In this example we will use a file provided with the ORIGAMI distribution. You can download MS file or you can find it in your ORIGAMI directory ( example_data/text ). Interactive output panel You can use any example file here as once you open the output window, all available plots will be shown in a list. In this case, the list contains all available items from a number of previous examples (e.g. annotating mass spectra, combining drift voltages, etc). If you click on any item in the list, its previously provided settings such as title, header, footnote information or plot parameters will be automatically rendered. Focusing on a mass spectrum first, you can see some useful information about the size of number of annotations, min/max ranges and its size . Check that item and click on the Export HTML button. You will be asked to provide a path where you would like to save the document. Make sure to check the Open in browser after saving checkbox. You can checkout a mass spectrum example here and heatmap example here .","title":"Getting started"},{"location":"user-guide/interactive-output/simple-output.html#exporting-interactive-figures","text":"ORIGAMI enables creation of HTML/JavaScript webpages which embed interactive versions of figures visualised in ORIGAMI. Practically all figures that you can generate in the desktop application can be also exported to a HTML document that can be shared with your supervisor, journal reviewers or collaborators for their in-depth interrogation. While this might seem like a bit of a gimmick, it makes sense to share the results with the scientific community in a manner more explorative than a simple static image. See here for some helpful encouragement ( Perkel and Weissgerber ).","title":"Exporting interactive figures"},{"location":"user-guide/interactive-output/simple-output.html#example","text":"In this example we will use a file provided with the ORIGAMI distribution. You can download MS file or you can find it in your ORIGAMI directory ( example_data/text ).","title":"Example"},{"location":"user-guide/interactive-output/simple-output.html#interactive-output-panel","text":"You can use any example file here as once you open the output window, all available plots will be shown in a list. In this case, the list contains all available items from a number of previous examples (e.g. annotating mass spectra, combining drift voltages, etc). If you click on any item in the list, its previously provided settings such as title, header, footnote information or plot parameters will be automatically rendered. Focusing on a mass spectrum first, you can see some useful information about the size of number of annotations, min/max ranges and its size . Check that item and click on the Export HTML button. You will be asked to provide a path where you would like to save the document. Make sure to check the Open in browser after saving checkbox. You can checkout a mass spectrum example here and heatmap example here .","title":"Interactive output panel"},{"location":"user-guide/processing/heatmaps.html","text":"Processing heatmaps All two-dimensional heatmaps can be processed to produce a more visually attractive figure. Video tutorial on how to process heatmaps Loading data Please have a look at Loading Text files . In short, you either drag-and-drop the text file in the main window of ORIGAMI-ANALYSE or go to File - Open IM-MS Text file . Example In this example we will use a file provided with the ORIGAMI distribution. You can download heatmap files or you can find them in your ORIGAMI directory ( example_data/text ). Opening processing panel The easiest way to process a heatmap is to find it in the Document Tree, right-click on it and select the Process... option. This will open a new window where you can select desired parameters and also execute the action. If you simply open the Processing window, it is not guaranteed ORIGAMI will know which heatmap you want to process, and will use the currently plotted heatmap as the data source. Of course, this is only a concern if you have more than one heatmap in the document. Processing Heatmaps can be processed in a number of ways, however the most common is to remove noise (using the threshold value) and normalize it (using the On/Off toggle). Setup your desired parameters and you can either replot the heatmap (data will not be added to the document) or process (data will be added to the document).","title":"Heatmap"},{"location":"user-guide/processing/heatmaps.html#processing-heatmaps","text":"All two-dimensional heatmaps can be processed to produce a more visually attractive figure.","title":"Processing heatmaps"},{"location":"user-guide/processing/heatmaps.html#video-tutorial-on-how-to-process-heatmaps","text":"","title":"Video tutorial on how to process heatmaps"},{"location":"user-guide/processing/heatmaps.html#loading-data","text":"Please have a look at Loading Text files . In short, you either drag-and-drop the text file in the main window of ORIGAMI-ANALYSE or go to File - Open IM-MS Text file .","title":"Loading data"},{"location":"user-guide/processing/heatmaps.html#example","text":"In this example we will use a file provided with the ORIGAMI distribution. You can download heatmap files or you can find them in your ORIGAMI directory ( example_data/text ).","title":"Example"},{"location":"user-guide/processing/heatmaps.html#opening-processing-panel","text":"The easiest way to process a heatmap is to find it in the Document Tree, right-click on it and select the Process... option. This will open a new window where you can select desired parameters and also execute the action. If you simply open the Processing window, it is not guaranteed ORIGAMI will know which heatmap you want to process, and will use the currently plotted heatmap as the data source. Of course, this is only a concern if you have more than one heatmap in the document.","title":"Opening processing panel"},{"location":"user-guide/processing/heatmaps.html#processing","text":"Heatmaps can be processed in a number of ways, however the most common is to remove noise (using the threshold value) and normalize it (using the On/Off toggle). Setup your desired parameters and you can either replot the heatmap (data will not be added to the document) or process (data will be added to the document).","title":"Processing"},{"location":"user-guide/processing/mass-spectra-annotation.html","text":"Annotating mass spectra Since version 1.1.2 it is possible to annotate mass spectra with custom labels (e.g. charge state , label ) and attached an arrow to highlight low-intensity species. Video tutorial on how to annotate mass spectrum Loading data Please have a look at Loading Text files . In short, you either drag-and-drop the text file in the main window of ORIGAMI-ANALYSE or go to File - Open MS Text file . Example In this example we will use a file provided with the ORIGAMI distribution. You can download MS file or you can find it in your ORIGAMI directory ( example_data/text ). Annotating There is a number of ways you can annote mass spectrum. The manual way involves opening an annotation panel and manually selecting peaks. You can also load annotations from a .csv file. Opening annotation panel Find the mass spectrum you would like to annotate in the Document Tree and right-click on it, then select Show annotations panel , a new window should show up: Adding an annotation Click on the Annotating: Off button so it switches to Annotating: On . Move your mouse to the mass spectrum window and hold CTRL on your keyboard while also dragging mouse over a peak (like during data extraction). When you release the mouse, a number of values will be added in the annotation panel (min/max band, position x, charge, intensity, etc) - all of which can be changed. When you are happy click on the Add annotation button. The annotation should appear in a list below. Repeat till you are fnished. Editing an annotation Select a annotation in the list below. Change any value. Click on the Add annotation button. Adding arrow to annotation Select a annotation in the list below. Uncheck the add arrow checkbox. Adjust values of position (x, label) and position (y, label) Click on the Add annotation button. Showing all annotations Click on the Show button and select appropriate option (e.g. Show m/z, intensity, charge). All annotations should be shown on the mass spectrum. Customising annotations You can adjust several parameters ( annotation color, arrow line thickness, label size, etc ) in the Customise annotations panel. You can open it by clicking on the Action button and selecting Customise other settings... . A new panel should open. Note: You will have to replot annotations as these settings do not automatically update. Duplicating annotations Sometimes you might have more than one mass spectrum a document that has a lot of the same peaks. You could manually re-add these, but there is a quicker way. Find the mass spectrum with annotations and right-click on it. Select Duplicate annotations... option. A new window will appear where you can select another document and mass spectrum to which annotations should be copied. Once you have selected, click Select and see if they have been copied. One thing to remember is that the intensity of the peaks in different peaks will vary so you have to fix the intensity of annotation label. To do this, open the annotation panel for newly copied annotations (Document Tree - Show annotations panel...) and click on the Action button. Once there, select Fix intensity option. Video tutorial on how to duplicate annotations","title":"Annotating mass spectra"},{"location":"user-guide/processing/mass-spectra-annotation.html#annotating-mass-spectra","text":"Since version 1.1.2 it is possible to annotate mass spectra with custom labels (e.g. charge state , label ) and attached an arrow to highlight low-intensity species.","title":"Annotating mass spectra"},{"location":"user-guide/processing/mass-spectra-annotation.html#video-tutorial-on-how-to-annotate-mass-spectrum","text":"","title":"Video tutorial on how to annotate mass spectrum"},{"location":"user-guide/processing/mass-spectra-annotation.html#loading-data","text":"Please have a look at Loading Text files . In short, you either drag-and-drop the text file in the main window of ORIGAMI-ANALYSE or go to File - Open MS Text file .","title":"Loading data"},{"location":"user-guide/processing/mass-spectra-annotation.html#example","text":"In this example we will use a file provided with the ORIGAMI distribution. You can download MS file or you can find it in your ORIGAMI directory ( example_data/text ).","title":"Example"},{"location":"user-guide/processing/mass-spectra-annotation.html#annotating","text":"There is a number of ways you can annote mass spectrum. The manual way involves opening an annotation panel and manually selecting peaks. You can also load annotations from a .csv file.","title":"Annotating"},{"location":"user-guide/processing/mass-spectra-annotation.html#opening-annotation-panel","text":"Find the mass spectrum you would like to annotate in the Document Tree and right-click on it, then select Show annotations panel , a new window should show up:","title":"Opening annotation panel"},{"location":"user-guide/processing/mass-spectra-annotation.html#adding-an-annotation","text":"Click on the Annotating: Off button so it switches to Annotating: On . Move your mouse to the mass spectrum window and hold CTRL on your keyboard while also dragging mouse over a peak (like during data extraction). When you release the mouse, a number of values will be added in the annotation panel (min/max band, position x, charge, intensity, etc) - all of which can be changed. When you are happy click on the Add annotation button. The annotation should appear in a list below. Repeat till you are fnished.","title":"Adding an annotation"},{"location":"user-guide/processing/mass-spectra-annotation.html#editing-an-annotation","text":"Select a annotation in the list below. Change any value. Click on the Add annotation button.","title":"Editing an annotation"},{"location":"user-guide/processing/mass-spectra-annotation.html#adding-arrow-to-annotation","text":"Select a annotation in the list below. Uncheck the add arrow checkbox. Adjust values of position (x, label) and position (y, label) Click on the Add annotation button.","title":"Adding arrow to annotation"},{"location":"user-guide/processing/mass-spectra-annotation.html#showing-all-annotations","text":"Click on the Show button and select appropriate option (e.g. Show m/z, intensity, charge). All annotations should be shown on the mass spectrum.","title":"Showing all annotations"},{"location":"user-guide/processing/mass-spectra-annotation.html#customising-annotations","text":"You can adjust several parameters ( annotation color, arrow line thickness, label size, etc ) in the Customise annotations panel. You can open it by clicking on the Action button and selecting Customise other settings... . A new panel should open. Note: You will have to replot annotations as these settings do not automatically update.","title":"Customising annotations"},{"location":"user-guide/processing/mass-spectra-annotation.html#duplicating-annotations","text":"Sometimes you might have more than one mass spectrum a document that has a lot of the same peaks. You could manually re-add these, but there is a quicker way. Find the mass spectrum with annotations and right-click on it. Select Duplicate annotations... option. A new window will appear where you can select another document and mass spectrum to which annotations should be copied. Once you have selected, click Select and see if they have been copied. One thing to remember is that the intensity of the peaks in different peaks will vary so you have to fix the intensity of annotation label. To do this, open the annotation panel for newly copied annotations (Document Tree - Show annotations panel...) and click on the Action button. Once there, select Fix intensity option.","title":"Duplicating annotations"},{"location":"user-guide/processing/mass-spectra-annotation.html#video-tutorial-on-how-to-duplicate-annotations","text":"","title":"Video tutorial on how to duplicate annotations"},{"location":"user-guide/processing/mass-spectra.html","text":"Processing mass spectra All mass spectra found in a ORIGAMI document can be processed in a way that reduced noise, smoothes peaks, or linearized the spectrum to reduce its size. Video tutorial on how to process mass spectra Loading data Please have a look at Loading Text files . In short, you either drag-and-drop the text file in the main window of ORIGAMI-ANALYSE or go to File - Open MS Text file . Example In this example we will use a file provided with the ORIGAMI distribution. You can download MS file or you can find it in your ORIGAMI directory ( example_data/text ). Raw mass spectrum Opening processing panel The easiest way to process a mass spectrum is to find it in the Document Tree, right-click on it and select the Process... option. This will open a new window where you can select desired parameters and also execute the action. If you simply open the Processing window, it is not guaranteed ORIGAMI will know which mass spectrum you want to process. Of course, this is only a concern if you have more than one spectrum in the document. Processing Spectral processing is taken in steps, and you can specify which action you would like to take. Crop spectrum: specify the min m/z and max m/z range spectrum should restricted to Linearize spectrum: linearize spectrum to have consistent spacing between points. There is a number of methods available that will change the way the spacing is calculated Smooth spectrum: specify the smoothing method (Gaussian or Savitzky-Golay) Baseline subtract: remove noise from the spectrum Normalize: normalize the spectrum to maximum value of 1 Once you are happy with your parameters, you can either replot the spectrum (data will not be added to the document) or process (data will be added to the document). Processed mass spectrum Note: If the Process button is disable, it probably means you just opened the Processing panel without specifying the mass spectrum - you can close it and try again from the Document Tree view.","title":"Mass spectrum"},{"location":"user-guide/processing/mass-spectra.html#processing-mass-spectra","text":"All mass spectra found in a ORIGAMI document can be processed in a way that reduced noise, smoothes peaks, or linearized the spectrum to reduce its size.","title":"Processing mass spectra"},{"location":"user-guide/processing/mass-spectra.html#video-tutorial-on-how-to-process-mass-spectra","text":"","title":"Video tutorial on how to process mass spectra"},{"location":"user-guide/processing/mass-spectra.html#loading-data","text":"Please have a look at Loading Text files . In short, you either drag-and-drop the text file in the main window of ORIGAMI-ANALYSE or go to File - Open MS Text file .","title":"Loading data"},{"location":"user-guide/processing/mass-spectra.html#example","text":"In this example we will use a file provided with the ORIGAMI distribution. You can download MS file or you can find it in your ORIGAMI directory ( example_data/text ). Raw mass spectrum","title":"Example"},{"location":"user-guide/processing/mass-spectra.html#opening-processing-panel","text":"The easiest way to process a mass spectrum is to find it in the Document Tree, right-click on it and select the Process... option. This will open a new window where you can select desired parameters and also execute the action. If you simply open the Processing window, it is not guaranteed ORIGAMI will know which mass spectrum you want to process. Of course, this is only a concern if you have more than one spectrum in the document.","title":"Opening processing panel"},{"location":"user-guide/processing/mass-spectra.html#processing","text":"Spectral processing is taken in steps, and you can specify which action you would like to take. Crop spectrum: specify the min m/z and max m/z range spectrum should restricted to Linearize spectrum: linearize spectrum to have consistent spacing between points. There is a number of methods available that will change the way the spacing is calculated Smooth spectrum: specify the smoothing method (Gaussian or Savitzky-Golay) Baseline subtract: remove noise from the spectrum Normalize: normalize the spectrum to maximum value of 1 Once you are happy with your parameters, you can either replot the spectrum (data will not be added to the document) or process (data will be added to the document). Processed mass spectrum Note: If the Process button is disable, it probably means you just opened the Processing panel without specifying the mass spectrum - you can close it and try again from the Document Tree view.","title":"Processing"}]}
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