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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 | ||
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### 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 | ||
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### 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 |