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update Changelog for v5.1.0 release
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AimeeD90 committed Dec 19, 2023
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Showing 1 changed file with 13 additions and 13 deletions.
26 changes: 13 additions & 13 deletions Changelog
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### Added
- Added the protein start and end positions to ions and peptides report.
- ProtXML reading parallelization.
- Added a new Extended Peptide column to the PSM report containing the flanking regions of peptides.
- Group-based FDR scoring capabilities that will rely on the group passed by MSFragger.
- Support for sCLIP isobaric tags.
- Supported IBT-16 isobaric tag
- Extended support for up to 32 isobaric labels.
- Added the 'minPepLen' control option for protein probability assignment
- Added the dbbin option to resue the prebuilt db.bin file

### Changed
- Rolled back the FASTA header checking for IonQuant.
- Improved the FASTA header detection and parsing.
- PTMProphet was updated to v6.2.0.
- The processing speed, including IO operations and database reading received a major upgrade (@guoci).
- The purity column will always be visible in the PSM table.
- Updated the MSstats report for individual data sets.
- Used unique+razor peptides only for PSM-protein level roll up
- For plex with 0 PSMs, let philosopher print a waring and exit normally
- Excluded decoys from protein quantification (protein.tsv)
- Removed the warning message for running 'workspace --clean' in a clean direcotry

### Fixed
- Updated razor mapping rules to reinforce classifying decoy razor proteins.
- Fixed a problem where protein names and genes would not be tagged with the decoy tag.
- Fixed a problem occurring when parsing custom database with headers starting with '>AT'
- Fixed a bug related to summed intensites in protein.tsv
- Fixed a bug causing empty intensities in msstats.tsv related with multiplex TMT11 data.
- Fixed a creash when there are non-zero TMT intensities and removelow > 0
- Updated the purity calculation

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