5. SpecStylus
The SpecStylus is a spectal annotation and notebooking tool.
- To open a SpecStylus window, select the "SpecStylus" menu item, and then click ‘Open Specstylus’.
- To create a new notebook, click File new and enter the notebook name.
- To add a new folder, click Add/New folder.
- This adds a new folder to the selected node.
- To set the filename, select the newly added folder and right click in the window. Select ‘Edit Info Bar’.
- Enter the filename and hit enter.
- Spectra and XICs can be added to the SpecStylus by first holding down CTRL key, and then left clicking in the spectrum or XIC window and dragging and dropping it to the SpecStylus window.
- The title can be changed by selecting the spectrum, right clicking in the window, and selecting edit title bar.
- Nodes can be rearranged by selecting the item, and then left clicking and dragging to a new location.
- Powerpoint, excel, and python files can be imported into the SpecStylus by drag and drop from the Windows explorer.
- You can also create links to OneNote pages in one of two ways
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Right click on the notebook tab in OneNote, and select "Copy link to page". In SpecStylus, select the node you wish to add the link to, right click, and select "Paste OneNote Link" from the context menu. The link will be added.
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Open OneNote, and navigate to the page you want to link to. In SpecStylus, select the node you wish to add the link to, right click, and select "Grab OneNote Link" from the context menu. The link will be added, and the page title will appear in the title bar.
- Double clicking each item opens it.
- XICs are displayed in ‘XICview Lite’.
- Here, XICs can be annotated with lines and text by selecting the appropriate widget and drawing the line, or clicking where to place the text.
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In addition, notes can be entered in the lower text box.
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Save button saves the XIC and all annotations. Select allows selecting objects; they can be deleted with the delete key, or repositioned with the mouse. Images can be exported with the SVG, PNG, or PDF buttons.
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When a spectrum is dragged to the SpecStylus, associated sequences and annotations are retained. The SpecViewLite toolbar has options for drawing lines, adding text, saving annotations, and exporting images. The mz tool allows zooming to a specific mass range. Typing 1, 2, or 3 will split the mass spectrum on the specified number of x-axes. If this is a processed spectrum (i.e. a custom spectrum processing script was applied to raw data), toggling ‘Q’ will turn processing on/off. The last tool sets the fragment ion label tolerance. Entering ‘0’ uses the instrument default (0.02 Da for FTMS instruments, 0.5 Da for all others).
- Opening a python script sets it as the currently active “Spectrum Processor”. This is discussed in more detail in the wiki page "Custom Spectral Processing".
- File – create new SpecStylus notebook, load and save notebooks.
- Add – adds a new folder, or auxiliary file (ppt, xls, py) to the selected node.
- Edit – edit or delete item.
- Export images – can export the current XIC or spectrum to ppt, or all spectra and XIC to powerpoint.
- PepCalc – open mzPepCalc
- Export Spectra – Makes a NIST compatible spectral library that can be used with the NIST search tool.