Last changed 2021-11-24

Improvements:

• Now showing progress bars during long running processes.

Notes:

• If you use Metaboseek for your research, please cite our paper!
• 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.

Last changed 2021-08-05

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.

Last changed 2020-12-30

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

Notes:

• SIRIUS path selection has moved to the SIRIUS options tab
• 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.

Last changed 2019-09-18

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.

Last changed 2019-08-04

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
• Get the newest Windows version here

New features:

• Metaboseek is now available as a Docker image, making it easy to install 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

Last changed 2019-06-21

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

Last changed 2019-05-24

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

Last changed 2019-04-09

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

Last changed 2019-03-25

Notes:

• Windows users: do not use the integrated updater to update to version 0.9.1. 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

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

Last changed 2019-03-14

Notes:

• This version can be installed in parallel with older versions even when using the Windows installer
• You cannot use the integrated updater to go from version 0.8.X to 0.9.X. Get the new Windows version here
• Linux/ MacOS users can update using this command: source("http://metaboseek.com/files/install_METABOseek.R")
• It is recommended to use Chrome as a browser. There are issues with Firefox when loading data into METABOseek

New features:

• Added SIRIUS analysis module
• Added option to change filename before saving tables
• Added option to see retention time in minutes (in Table Filter box)
• MS2 scan search can now be set to only match MS2 scans with the feature with closest RT (within tolerance), instead of all features within RT tolerance.
• Additional options to simplify networks (can now use two conditions for edge merging concurrently)
• Freestyle data plotting in quickplots now applies active filters to the feature table items before plotting. Also increased limit for interactive plots from 1000 to 2000 data points.
• Changed and improved peak picking algorithm
• Added option to get peak intensities for tables with mz and rt values
• New "Fast peak shapes" analysis option is orders of magnitude faster than the older version

Bug fixes:

• Fixed issue with saving tables that contain commas (e.g. in comments) and improved speed of saving tables
• Tables no longer "wrap around" (which led to going back to row one when hitting the bottom of a table page)
• Fixed bug in Network viewer that caused the plot to frequently crash in overview mode
• Old/slow peak shapes analysis is now faster than it used to be thanks to multithreading

Last changed 2019-02-19

New features:

• Added m/z calculator to Analyze Table Tab: Calculate m/z of different charge states for molecular formulas
• mzMatch function added to Analyze Table Tab: Find m/z values in Feature table that match compunds in a database
• METABOseek options are no longer reset when updating through the internal updater
• Changes to welcome page layout

Bug fixes:

• Fixed rescaling and performance issue in multi EIC Tab when using MS data layouts for subsets of MS data files

Last changed 2019-02-04

New features:

• Added Venn Diagrams
• Added volcano plots in Quickplots
• Added customizable subtitles in grouped EIC plots
• Added "Load data" button to dashboard header
• Added an early version of peak picking (for targeted metabolomics) to Analyze Table Tab

Bug fixes:

• Fixed issue when feature rt was outside a file's rt range
• Fixed multiple crash issues when making or simplifying a METABOseek network and when viewing MS2 spectra
• Fixed issue with networking when applying a noise threshold

Last changed 2019-01-18

Renamed MOSAiC to METABOseek

New features:

• Table analysis: Added ANOVA-like analysis

Bug fixes:

• Fixed issue where comments were not fixed in column 3 of the feature table
• Fixed file naming issue for saving tables when using "Save locally"
• Applying log10 to normalized intensities now also works in xcms post-processing
• Fixed y-axis rescaling issue when RT correction was selected in grouped EICs

Last changed 2019-01-08

New features:

• MS2 Browser: Added button to find all MS2 scans for features in Feature Table (results are added to Feature Table)
• MS2 Browser: Added functionality to create, browse and simplify MS2 networks
• Analyze Table: Added option to apply log10 during normalization of intensity values

Bug fixes:

• Fixed crashing issue when filtering for strings in columns of the Feature Table

Coming soon:

• Saving and loading METABOseek sessions from .METABOseekXML files

Released 2018-11-09

Usability upgrades:

• xcms analysis saves a version of the resulting feature tables now before applying (potentially very time-consuming) post-processing (e.g. peak shapes analysis)
• Molecular formula prediction on any peak in any spectrum (select "spectrum" as source in the Molecular Formula tab, optionally select "Calculate automatically" and SHIFT + click on a peak in any MS1 or MS2 spectrum). NOTE: currently will use the marker on the last spectrum that the cursor was moved over, not necessarily the last marker that was set.
• Export individual spectra as .pdf or .tsv (tab-separated peak list)
• Rescale EICs to the maximum intensity across all EIC groups in Grouped EICs tab ("Rescale" checkbox)

Bug fixes:

• Comments column now gets imported correctly when loading a table with an all-empty comments column
• METABOseek no longer crashes when folder selection is canceled in XCMS module
• Fixed problem with MS browser when only a single MS data file was loaded

Coming soon:

• Saving and loading METABOseek sessions from .METABOseekXML files

Released 2018-10-18

Bug fixes:

• METABOseek no longer crashes when switching Feature Tables when certain filters are selected
• The columns that can be selected for filtering are now updated when new columns are added to a Feature Table
• When entering filter values, the input field is no longer automatically deselected

Released 2018-10-15

New in this version:

• New start page with update news and quick access to data loading opotions
• Option to show small EIC plots
• Feature Table selection remains highlighted when clicking elsewhere in the program
• When a project folder is selected, Feature Tables can be saved there directly
• Complete internal do-over that should improve performance and future expansion