All notable changes to RawTools will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
- 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).
- 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.
- 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.
- When processing a non-FAIMS file, if the faimsMgf option is enabled, it will simply re-write the whole MGF.
- 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).
- 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).
- Added functionality for TMTPro reagents.
- Fixed a bug which crashed the command line help in Linux and MacOS.
- 2.0.0 contained a bug which prevented RawToolsViz from opening any data files. This has been fixed.
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The command line interface has changed to streamline workflows and align the CLI with the GUI. There will no longer be "modes" which you need to call before parameters. e.g. You do not need
parseorqcafter RawTools on the command line anymore. This means you can perform parsing and qc at the same time. The interface will be slightly different in terms of what parameters are called, so be sure you check outRawTools -help. -
IdentiPy is no longer supported as a search engine. Database searches are now only carried out using X!Tandem. We plan to switch this to SearchCLI in the future to allow users to select a search engine of their choice.
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The GUI is now intergrated and will be part of all releases. To use it just open RawToolsGUI in the RawTools directory.
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Data visualization is now available as part of RawTools via RawToolsViz.exe
- We have changed the internal settings of RawTools so output data files always use decimal dots rather than decimal commas (e.g. 1.234 vs 1,234). Previously decimal commas were sometimes the default depending on the system language. This decision was made because some database search engines are not able to properly parse MGF files with decimal commas. If this impacts your downstream workflow in a negative way, please let us know and we will try to make this change user-specified rather than a default.
- There was a bug that resulted in crashes during quantification. This was introduced with the reporter mass error reporting. It has been fixed.
- MGF files in v1.4 were found to be incompatible with MS-GF+. This has been fixed.
- Fixed a bug in which RTINSECONDS, as reported in the MGF file, was actually in minutes. It is now in seconds.
- We have streamlined the processing workflows to improve performance, and RawTools can now run on multiple processors. Hopefully this will speed up the processing of very large files. [issue6]
- Occasionally there are scans with corrupt headers or which are otherwise not linked to their precursor/dependent scan(s) (e.g. a MS2 scan which has no master scan associated with it in the file). This is pretty rare, but when it comes up RawTools now detects such "orphan scans" and prints out a report to the console letting you know which scans are affected. These scans are not included in the output tables, so you can check them manually if desired to make sure they are not critical to your analysis.
- Relative paths are now supported for all arguments.
- Precursor peaks are now extracted based on picked m/z rather than monoisotopic m/z.
- The next release will add a new "logdump" function, which outputs the raw file instrument log to a text file. Use it like this:
RawTools logdump -f [path to raw file]RawTools logdump -d [directory in which to get log files from all raw files]Pretty much everything about how the instrument was operating is in there, scan by scan, from capillary temperature to lens voltages to turbopump lifetimes, etc.
- Previously the total number of scans reported in the metrics was incorrect. This has been fixed, though in the event of orphan scans (as described above) those scans will not be counted towards the total.
- MGF files are now compatible with MS Amanda.
- Users with heightened Windows security settings might have difficulty running RawTools since it is acquired via internet download. The solution has been to modify the RawTools.exe.config file to allow the app to load assemblies from remote locations. This has come up enough that we've decided to make the change permanent. [issue5]
###Fixed
- The program will now give a warning when a filename provided via -f does not exist (as opposed to simply crashing).
- We came across a file with an apparently corrupted MS3 scan in it which was cause RawTools to crash. The MS data for the scan was in the raw file, but the meta data was incomplete. To address this, the scan lists RawTools uses to process are now built off of the scan dependents found in the raw file meta data. This means scans which are missing meta data will not appear in the output data table. Note that these occurances are rare, and we are planning to add a text output to alert the user when this happens.
- The examples have been updated. There are now two sections to the examples function: --interface and --modifications.
- MS3ScanRate was not referencing the correct data. Is fixed now.
- Fixed a bug which caused a crash when MS scan data was absent or corrupted for a scan.
- Fixed a bug where precursor charge state and monoisotopic m/z was not refined when the only output was an MGF file.
- Fixed a QC bug in which the -N argument was always used as the number of ms2 spectra, even if it was greater than the actual number of spectra in the raw file.
- Fixed a bug in the master scan index would not be found for some instruments or Tune versions.
- RawTools is unable to properly process files from very short duration acquistions. Problems seem to often come up with handeling precursor peaks. As a quick workaround, metrics are not reported for precursor peaks when this issue occurs. A future fix will address the problem more thoroughly. [issue2]
- MS1 isolation interference calculations added to parse and qc outputs.
- Refinement of precursor charge state and monoisotopic mass. This can be invoked using
-Ras an argument. This can be important if monoisotopic precursor selection is turned off in your instrument method. The refinement works by creating a list of possible charge states for each precursor based upon isotope neighbors, then generating a set of averagine isotope envelopes representing the possible monoisotopic masses of the precursor m/z value and nearby isotope peaks. Scoring is based on the Bhattacharyya distance between the isotope envelope of the observed spectrum and the theoretical averagine spectrum.
- Added support for X! Tandem as a search engine.
- Chromatograms of raw files can be exported as tab-delimited text files using
--chroas an argument. SeeRawTools.exe parse --helpfor more info.
- The
-iargument for invoking an IdentiPy search has been deprecated and will not be available in future releases. Instead, please use-s identipyto invoke an IdentiPy search. Other IdentiPy-related arguments will remain as-is.
- The code for parsing IdentiPy results and calculating identification-based metrics has been reworked to facilitate compatibility with X!Tandem results files. This should have no impact upon end-users, but will make it easier to add support for other search engines in the future if it is desired.
- Fixed a bug which occurs when no variable modifications are specified.
- Everything! But that isn't very informative, so check out the wiki page to learn about RawTools.