Metaboseek

Get Metaboseek!

Metaboseek is here for all platforms, and you can even try it online (may take up to a minute to load).

Windows

Metaboseek for Windows is available as a convenient installer or as .zip file that contains everything you need!

 

Linux/macOS

Follow instructions to get Metaboseek for Linux and macOS

Update Log
Version 0.9.6.4

Last changed 2020-4-02

New features:

  • You can now choose between different layouts when displaying molecular networks

Improvements:

  • Major update to the documentation (online and R package vignette)

Bug fixes

  • Fixed bug when saving filtered Feature Tables in mskFT format when using sorting
  • Corrected the dates (year) on version news (this document)

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.
Version 0.9.6

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.
Version 0.9.5

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
Version 0.9.4

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
Version 0.9.3

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
Version 0.9.2

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
Version 0.9.1

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
Version 0.9.0

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
Version 0.8.6

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
Version 0.8.5

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
Version 0.8.4

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
Version 0.8.3

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
Version 0.8.2

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
Version 0.8.1

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
Version 0.8.0

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
Note: There are currently problems when loading data in Firefox - please use a different browser (Chrome, Safari...) until this has been fixed.