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

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
  • -s, --stdout option addition for writing to standard out (mostly for Windows)

Changes in ThermoRawFileParser 1.3.2 (Oct 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 (Sep 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 (Aug 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 (Mar 2. 2020):

  • Minor change in biocontainer docker file

Changes in ThermoRawFileParser 1.2.1 (Feb 14. 2020):

  • Bug fixes
  • Additional XIC input validation

Changes in ThermoRawFileParser 1.2.0 (Feb 6. 2020):

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

Changes in ThermoRawFileParser 1.1.11 (Sep 25. 2019):

  • Addition of more Thermo instrument models

Changes in ThermoRawFileParser 1.1.10 (Aug 23. 2019):

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

Changes in ThermoRawFileParser 1.1.9 (Jul 2. 2019):

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

Changes in ThermoRawFileParser 1.1.8 (Jun 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 (Jun 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
  • added extra log statement with the number of scans being processed
  • fixed max and min charge bug in json metadata output