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