ReleaseNotes (original) (raw)

ReleaseNotes

Changes in ThermoRawFileParser 2.0.0-dev (Oct 27. 2025):

• Code is fully migrated to .NET 8, thus, Mono dependency is obsolete
• Added an action for automatic building and testing on all code changes
• Added an action to produce self-contained and framework-based binaries for all major platforms on release
• Parquet format is updated to version 0.2
• Charge state array can be included in mzML and MGF output
• Precursor ion intensity in MGF output
• Support for precursor ion and neutral/loss gain scans
• Cleaner error messaging and improved error handling
• Introduce the latest instrument CV terms (PSI-MS 4.1.204)

Changes in ThermoRawFileParser 1.4.5 (Oct 14. 2024):

• Fixing CV annotations in PROXI format

Changes in ThermoRawFileParser 1.4.4 (May 10. 2024):

• Speedup the processing of files when only some MS levels are written to the output (closes #176)
• Handling of raw files missing the supplementary activation flag (closes #175)
• Using CVTerm "Orbitap" instead of "FTICR" for Orbitrap-based instruments (closes #177)
• Unification of command line arguments (#179), shout-out to @xjasg
• Fixing metadata output for files missing MS part, shout-out to @wolfgangcolsman
• Minor fixes to mzML output and cleaning unused code

Changes in ThermoRawFileParser 1.4.3 (September 15. 2023):

• Added support for Thermo Astral RAW files
• Update Thermo .NET assemblies to version 5.0.0.93

These two changes allow for converting RAW files produced by Thermo Astral mass spectrometer

• Added support for PRM files without MS1 (shout-out to @lazear, fixes #163 #164)

Files lacking MS1 scan completely (such as, for example, PRM runs) can be processed

• Fix for negative values in isolation window (fixes #162)

A bug that results in negative isolation width for some RAW files is fixed

• Complete support for raw files without MS data (only for MzML and metadata output) (shout-out to @wolfgangcolsman, fixes #157)

Files without MS data, for example, only UV chromatograms are supported. MzML and metadata outputs are supported, since MGF and Parquet contain only MS-related infromation

• Added expected runtime to metadata output (shout-out to @wolfgangcolsman, fixes #166)

New value expected runtime is added to metadata output

Changes in ThermoRawFileParser 1.4.2 (February 11. 2023):

• Proper handling of precursors in decision tree methods from tribrids

RAW files acquired on tribrid platform with methods employing so-called decision tree have unusual precursor information. The fix implements proper handling of such files. Refer to Issue 147 for details.

• Output file extension always follows the file format and (if employed) gzip compression

Refer to Issue 148 for details.

• Support for input files provided as symlinks

Earlier versions of TRFP failed if the input argument was a symlink. Currently, TRFP can detect such cases and resolve symlink target to process it. Refer to Issue 146 for details.

• Support for single file output for xic subcommand

Added an option -b|--output_file allowing control over output file name. Works only for single file input. The short command line key -b is the same as for other subcommands. **NOTE This change breaks command line compatibility with earlier versions - -b was previously used to produce base64-encoded output; now the short key for base64-encoding is -6, the long key compatibility is preserved.

• Allowing optional field comment in XIC input json file

The comment field is preserved during XIC extraction and can be used as a key to identify different XICs in the output.

• Thermo .NET assemblies were updated to version 5.0.0.88

Changes in ThermoRawFileParser 1.4.1 (October 10. 2022):

• Files with missing trailer information can be processed

Some RAW files have a missing part of the scan named trailer, now these files can be processed Issue 141. Please, note that a trailer contains technical information necessary for some of the functions, such as monoisotopic mass, charge, etc. These might not work properly for the scans with the missing trailer.

• Using dedicated CV term for mzML output

Now ThermoRawFileParser uses CV terms added around august 2021, as a consequence some downstream tools released before this date might fail to process files generated by ThermoRawFileParser. The solution is to update downstream tools to the recent version Issue 112

• Support for all possible MS levels in MGF output

All MS levels are included in the output, previously only up to MS3; the change mirrors earlier change in mzML output

• Proper processing of empty RAW files

The program does not crash when empty (0 MS scans) file is provided Issue 144

• Fixed a bug in handling isolation offset in mzML output

If the isolation offset feature (isolation window shifted compared to the isolated mass) was used during the data acquisition, isolation window borders were calculated incorrectly

• Refining OS exit codes reporting and "warning as error" key

The exit code now shows the number of errors encountered during processing, i.e. non-zero code indicates possible problems. If a key -w --warningsAreErrors is specified, the exit code is the number of warnings and errors (warnings still will be reported as warnings in the log) Issue 140 Some of the error and warning messages have been rewritten

• More logging levels

Two new logging levels are added. Warning (3) omits information messages, Error (4) omits information and warning messages

• Exit codes and logging work in the same way for subcommands as well

Changes in ThermoRawFileParser 1.4.0 (June 10. 2022):

• Precursor intensity was added to mzML files

Precursor intensity is now included in mzML output, the output should be fairly similar to ProteoWizard. However, the intensity value should be used with caution, see Issue 125 and cited issues.

• Support for all possible MS levels

All MS levels are included in the output, previously only up to MS3; mapping precursor scans using new method Issue 126

• -x switch has reversed its meaning

When -x is defined reference and exception data will be excluded from the output, by default they will be included. Similar to Proteowizard.

• Plain mzML (non-indexed) is forced when using -s and mzML format

When using output to STDOUT and mzML format, the format will be always non-indexed Issue 118

• Updated ontology terms for ionization methods (HUPO PSI-MS version 4.1.79)

Added / updated ionization methods, Issue 128 Thank you, @abdelq

• Switch to include noise and baseline data (-N)

With the new switch -N|noiseData noise and baseline data can be included in mzML output Issue 130 Thank you, @GeorgWa

• Spectral points are sorted by mass

Issue 117

• Metadata, format, and logging switches recognize both numeric and string values of parameters

It is possible to use both text representation (case-insensitive) and numeric representation for switches, i.e. -f mzml and -f 1 are the same Issue 121

• Support for isolation window offset

Added support for isolation offset feature (isolation window shifted compared to the isolated mass) when it is used during the data acquisition

Changes in ThermoRawFileParser 1.3.4 (April 20. 2021):

• Disable peak picking for specified MS levels
• Rollback of ThermoRawFileParser CV term until downstream tools update their PSI-MS CV

Changes in ThermoRawFileParser 1.3.3 (April 01. 2021):

• Removed BOM prefix in indexed mzML output
• Addition of MS:1000576 (no compression) CV term when no compression is used
• Same metadata output for both TEXT and JSON formats
• FAIMS compensation voltage output
• Thermo libraries upgrade to 5.0.0.71
• -s, --stdout option addition for writing to standard out (mostly for Windows)

Changes in ThermoRawFileParser 1.3.2 (October 02. 2020):

• Flag -x include reference and exception peaks
• SPS masses are included as precursors in mzML
• Ignore all not .raw files when processing folder
• Updates in instrument and detector mapping to PSI-MS CV terms

Changes in ThermoRawFileParser 1.3.1 (September 08. 2020):

• Select MS levels to be written to the file (-L|--msLevel command line argument)
• Write precursor scan number in the TITLE of MGF file (-P|--mgfPrecursor command line argument)
• Correct version of the assembly
• Correct typo in -a flag description

Changes in ThermoRawFileParser 1.3.0 (August 26. 2020):

• Able to extract additional detector data - UV, PDA, pressure chromatograms, PDA spectra (new command line argument -a|--allDetectors)
• Fix instrument mapping and adding new instruments (Exploris series, ID-X etc)
• Update PSI-MS ontology version
• Fix empty output directory bug

Changes in ThermoRawFileParser 1.2.3 (May 4. 2020):

• Default centroiding of segmented scan data
• Thermo libraries upgrade

Changes in ThermoRawFileParser 1.2.2 (March 2. 2020):

• Minor change in biocontainer docker file

Changes in ThermoRawFileParser 1.2.1 (February 14. 2020):

• Bug fixes
• Additional XIC input validation

Changes in ThermoRawFileParser 1.2.0 (February 6. 2020):

• Addition xic and query subcommands (beta)
• Minor bug fixes

Changes in ThermoRawFileParser 1.1.11 (September 25. 2019):

• Addition of more Thermo instrument models

Changes in ThermoRawFileParser 1.1.10 (August 23. 2019):

• input directory argument addition
• silent logging mode
• metadata output file argument addition
• error handling improvements

Changes in ThermoRawFileParser 1.1.9 (July 2. 2019):

• no zlib compression flag addition for the binary data in the mzML output

Changes in ThermoRawFileParser 1.1.8 (June 18. 2019):

• addition of a progress indicator
• in MGF output: if no charge is found, no CHARGE header instead of CHARGE=0+

Changes in ThermoRawFileParser 1.1.7 (June 4. 2019):

• reports the monoisotopic mass as precursor mass when available
• fixed MS3 precursor scan not found
• fixed wrong scan type annotation (centroid/profile) in mzML output
• log file appender is commented out
• addition of --version argument
• updated thermo library to version to 5.0.0.6
• added extra log statement with the number of scans being processed
• fixed max and min charge bug in json metadata output