RawTools 2.0.7

Changes

• Fix a major issue with parse and qc triggering.
• Fixed an issue that would cause QC to fail if no or insufficient search results were found.

RawTools 2.0.6a

Changes

• Fixed a bug where the -p flag had to be active to run functions such as -chro or -mgf.
• Fixed various bugs related to the handling of raw files containing only MS1 scans.
• From a user request, added a function to output MS1 scan data to a text file (-asd flag).

RawTools 2.0.6

Changes

• Removed the 'MS1 only' mode. RawTools will now automatically detect if it is an MS1 only file and proceed based on the appropriate program flags.
• Added an XIC function (-xic) that allows users to output chromatogram data based on specified mass/tolerance settings.

RawTools 2.0.5

Changes

• Added the ability to process files with only MS1 scans (-ms1 flag).
• Added the ability to create MGF output for individual CV values in FAIMS data (-faimsMgf).
• Added a FAIMS CV column to the parse and quant matrix.
• Added FAIMS values to the metrics output, if available.

Known bugs

• When processing a non-FAIMS file, if the faimsMgf option is enabled, it will simply re-write the whole MGF.

2.0.4

[2.0.4] 2022-02-01

Changes

• Updated ThermoRawFileReader to version 5.0.0.71.
• Added compatibility for TMT 18-plex reagents.
• Added an MGF writer for different MS levels ('-mgfLevels' flag, see help).

Fixed

• Typo in 'MedianMs1IsolationInterference' in QC output (Issue #70).
• Added an option to output the version number with --version (Issue #65).
• Added an option to output different MS levels to MGF (Issue #69).

2.0.3a

This release fixes a small bug where the improper fragment mass was used during X!Tandem searches with the QC function.

2.0.3

Change

• Added functionality for TMTpro (16-plex) data processing.

2.0.2

Fixed

• Fixed a bug which crashed the command line help in Linux and MacOS in v2.0.0 and 2.0.1

2.0.1

Fixed!

• RawTools 2.0.0 had a fatal bug in RawToolsViz that was introduce during the release build. Basically RawToolsViz would not open anything. This is fixed now! (please note that QC and parse visualization are still not working very well in Linux, but we will try to address this soon).

Changes

• Please see changes under RawTools 2.0.0 below to see what is new in v2.

2.0.0

Attention [2019-07-04]

• Do not download v2.0.0. It contains a bug which prevents RawToolsViz from opening data files. Please get v2.0.1 instead.

Changes

• A lot has changed since v1.4.2!
• The command line interface has been updated and streamlined. While this breaks compatibility with old versions, we think the improvements are worth it. Parsing and QC are no longer separate operations, but can be performed at the same time. As such, there are no longer "parse" and "qc" modes to invoke. We have made efforts to preserve most of the original arguments as they were, so there shouldn't be too much to update if you use RawTools as part of a script. For help with this new interface, see RawTools -commands.
• We have now integrated data visualization into the tool itself. The new RawToolsViz.exe allows for visualization of QC and parse data and RawTools-generated chromatograms, and exploration of Thermo .raw files themselves. While the .raw file exploration has only been extensively tested in Windows, it should be compatible with Linux and Mac systems as well.
• Some metrics have been renamed to align the naming schemes used in the various data files (parse, qc, metrics). Because of this, the Shiny app may not work anymore. It is unlikely the app will be updated as visualization can now be carried out locally.
• New metrics have been added to QC output, including the number of cycles across the average peak profile, median peptide hyperscore and cutoff hyperscore used for FDR.