ReleaseNotes

ReleaseNotes

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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

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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)

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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

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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

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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

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Changes in ThermoRawFileParser 1.2.3 (May 4. 2020):

• Default centroiding of segmented scan data
• Thermo libraries upgrade

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Changes in ThermoRawFileParser 1.2.2 (Mar 2. 2020):

• Minor change in biocontainer docker file

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Changes in ThermoRawFileParser 1.2.1 (Feb 14. 2020):

• Bug fixes
• Additional XIC input validation

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Changes in ThermoRawFileParser 1.2.0 (Feb 6. 2020):

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

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Changes in ThermoRawFileParser 1.1.11 (Sep 25. 2019):

• Addition of more Thermo instrument models

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Changes in ThermoRawFileParser 1.1.10 (Aug 23. 2019):

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

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Changes in ThermoRawFileParser 1.1.9 (Jul 2. 2019):

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

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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+

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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 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

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