v0.9.9

Improvements:

Now showing progress bars during long running processes.

Notes:

If you use Metaboseek for your research, please cite our manuscript!
Metaboseek requires R 4.1 and bioconductor 3.13 (included in installer for windows).
Get the newest version here
If zooming in or out with double click does not work in spectrum or EIC plots, try CTRL + click. To zoom out of subnetwork views, Z + click is an alternative to double click in the network plot.

v0.9.8.1

New features:

Tables in mzMINE Aligned Peak List, MS-DIAL Alignment Result and MetaboAnalyst LC/MS Peak Intensity Table formats are recognized and reformatted during data loading without additional settings.
Calculate M value to find best features to use for normalization
New normalization options
Added option to restrict maximum cluster size in Network module

Improvements:

Update to SIRIUS module (works with SIRIUS >= 4.5)
p-value adjustment method can now be selected (in global settings)
Cleaned up the user interface for more clarity

Bug fixes

Special characters in column names no longer cause problems in Freestyle plots
Less error messages, more stable network viewer

Notes:

Metaboseek now requires R 4.1 and bioconductor 3.13.
Get the newest version here
If zooming in or out with double click does not work in spectrum or EIC plots, try CTRL + click. To zoom out of subnetwork views, Z + click is an alternative to double click in the network plot.

v0.9.8

New features:

Tables in mzMINE Aligned Peak List and MetaboAnalyst LC/MS Peak Intensity Table formats are recognized and reformatted during data loading without additional settings.
Calculate M value to find best features to use for normalization
New normalization options
Added option to restrict maximum cluster size in Network module

Improvements:

Update to SIRIUS module (works with SIRIUS >= 4.5)
p-value adjustment method can now be selected (in global settings)
Cleaned up the user interface for more clarity

Bug fixes

Special characters in column names no longer cause problems in Freestyle plots
Less error messages, more stable network viewer

Notes:

Metaboseek now requires R 4.1 and bioconductor 3.13.
Get the newest version here
If zooming in or out with double click does not work in spectrum or EIC plots, try CTRL + click. To zoom out of subnetwork views, Z + click is an alternative to double click in the network plot.

v0.9.7

New features:

Label finder module in Feature Table Action -> Analyze Table allows finding of isotope labeled molecular features
Ratio Plot module in Data viewer -> Ratio Plot allows plotting ratios between molecular features across sample groups
Imputation and normalization of data can now be controlled separately
Option to export a Feature Table in MetaboAnalyst Peak Intensity Table format.

Improvements:

You can now choose between different layouts when displaying molecular networks
Major update to the documentation (online and R package vignette)
Rename the current Feature Tables
Download as pdf vector graphic for Quickplots and some other plots, plus option to download plot data.
MS2 pattern finder can now find neutral losses, too.

Bug fixes

Fixed bug when saving filtered Feature Tables in mskFT format when using sorting
Corrected the dates (year) on version news (this document)
Various improvements to molecular formula calculation, including fix to ppm calculation
Fixed issue with intensity column selection in Feature Table Actions -> Filter Table
MS2 pattern finder now more robust to unexpected input

Metaboseek version 0.9.6

New features:

Metaboseek keeps track of most analysis steps now, and the processing history can be viewed in the app.
New file format (.mskFT) allows to save and load Feature Tables with processing history and other settings.
New file format (.mskg) allows to save and load molecular networking results with processing history and other settings.
Molecular features from a Feature Table can now be mapped onto an existing molecular network (even when generated from other data), matching features with similar rt, mz and / or MS2 fragmentation patterns.
Metaboseek sessions can now be saved into a single file (.msks) and loaded back in. See documentation for details
Added functionality to search for MS2 fragment patterns across all loaded files
In MS2 networking, added option to ignore small fragment ions (below 100 mz, often dominant phosphate peaks) for testing purposes

Improvements:

Added option to calculate peak areas (instead of mean intensities) for Mseek intensities while running xcms script
Network appearance (node positions) is now persistent when zooming back out into overview mode
xcms script was rewritten to allow tracking of processing steps
xcms settings are now saved in the settings subfolder of a project folder to keep them separate from analysis results
File names in selection menus now wrap so they can be read in full even when very long

Bug fixes

Sirius results can now be loaded if no fingerID results present
Fixed calculation of peak areas when using the integrated intensity calculation with option "Peak areas"
Fixed colorrange issue with NA values in Network plots

Notes:

Get the newest version here
If zooming in or out with double click does not work in spectrum or EIC plots, try CTRL + click. To zoom out of subnetwork views, Z + click is an alternative to double click in the network plot.

Metaboseek version 0.9.5

Notes:

• The name of the package and the repository is now Metaboseek (previously: METABOseek).
• Folder selection dialog for xcms analysis when using Windows has been changed to match other folder selection dialogs and is now the same as when using Linux or Mac OS.
• Spectrum averaging is now done using the MassTools::mergeMS() function in all instances (slightly different averaging results than before). Spectrum comparison functions (for molecular networking) have been modified and moved to the MassTools package

New features:

• Metaboseek is now available as a Docker module, making it easy to install it on desktops or servers as a webservice to showcase your data. More information available in the Metaboseek documentation.

Improvements:

• More options for node coloring in networking module, and more consistent color scales
• Side buttons for export and molecular formula calculation added to the new Spectrum viewer module
• Added more user friendly selection options for xcms output files in the xcms module
• xcms runs now save SessionInfo (listing the versions of all packages loaded during the xcms analysis to help with reproducibility)

Bug fixes

• Major bug fixed: When adding comments to a table, switching to a different table immediately afterwards no longer overrides rows of the newly selected table.
• Changing control group in pre-processing in xcms no longer causes Metaboseek to get stuck
• Selecting folders without MS data files in xcms module no longer causes Metaboseek to crash

METABOseek version 0.9.4

Notes:

Windows users: integrated updater is deactivated until further notice. Get the newest Windows version here

New features:

Added a peptide annotation app that can be started from R with runPeptideApp(). Allows annotation of MS2 spectra with fragment ions and variable modifications.
Added a draft vignette with information about METABOseek for developers

Improvements:

Revamped function documentation and cleaned up code

METABOseek version 0.9.3

Notes:

Windows users: do not use the integrated updater to update to version 0.9.3. Get the newest Windows version here
Problems with Firefox are fixed. Chrome or Firefox are recommended for running METABOseek

New features:

New molecular formula prediction module based on the Rdisop package, with many additional filter options to get reasonable formulas
Molecular formula prediction can now be used on-the fly in the MS2 Spectrum view (next to the MS2 scan table). This improved Spectrum viewer will soon be used throughout the app.
Batch molecular formula prediction for all features in the feature table

Improvements:

SIRIUS module UI changed again and now shows proposed molecular structures.
Metaboseek now sends all selected MS2 spectra individually to SIRIUS, which should improve results especially when different fragmentation energies were used.
Database for FingerID searches can be specified
MS2Browser UI changed again, changed looks of Network visualization (e.g. log scale used for coloring nodes by numeric values)
Added more database options to MzMatch functionality
Improvements to code structure that will make it easier to add functionality in the future

Bug fixes:

Fixed crashes in VennDiagramm section
Fixed various issues with SIRIUS modules

METABOseek version 0.9.2

Notes:

Windows users: do not use the integrated updater to update to version 0.9.2. Get the newest Windows version here
It is recommended to use Chrome as a browser. There are issues with Firefox when loading data into METABOseek

New features:

Secondary grouping to MS data views, allowing to color EIC traces by custom groups instead of by file
Recently used project folders can be loaded quickly without browsing for them
Additional EIC plotting options: raise EIC (makes 0 intensity scans visible in EICs), relative Intensities (which shows % relative intensity instead of absolute values on y-axis)
New FeatureReport module in MS2Browser, allowing to make one-page summaries on a molecular feature with EICs, MS1 and MS2 scans plus SIRIUS fragmentation tree and fragment annotation
Feature Table can be exported as inclusion or exclusion list for Thermo QE(-HF) instruments

Improvements:

SIRIUS module UI changed and shows more results for fragmentation trees
MS2Browser UI changed, increased size of Network visualization

Bug fixes:

Comments made right before filtering the feature table are no longer ignored by filters

Version 0.9.1

Notes:

It is recommended to use Chrome as a browser. There are issues with Firefox when loading data into METABOseek

Bug fixes:

Sorting MS2 scan list table now works as it should
Fixed errors occuring when using the peak picking module
Internal update module is now less likely to cause problems when updating METABOseek
Undefined page number in Feature Table (e.g. deleting page number before entering a new one) no longer crashes METABOseek