Added the 'minPepLen' control option for protein probability assignment
Added the dbbin option to resue the prebuilt db.bin file
Changed
Used unique+razor peptides only for PSM-protein level roll up
For plex with 0 PSMs, let philosopher print a warning and exit normally
Excluded decoys from protein quantification (protein.tsv)
Removed the warning message for running 'workspace --clean' in a clean direcotry
Fixed
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 crash when there are non-zero TMT intensities and removelow > 0
Updated the purity calculation
v5.0.0
11 months ago
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 option (based on the group labeled passed by MSFragger).
Support for sCLIP isobaric tags.
Changed
Rolled back the FASTA header checking for IonQuant.
Improved the FASTA header detection and parsing.
PTMProphet was updated to v6.2.0.
Faster processing speed and reduced memory usage due to major improvements in IO operations and database reading (@guoci).
The purity column will always be visible in the PSM table.
Updated the MSstats report for TMT data, making them compatible with MSstats and MSstats-PTM.
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.
v4.8.1
1 year ago
Added
FASTA header verification for IonQuant
Changed
New version annoucements will happpen for all updates, including minor changes
Fixed
Fixed an issue that would not udpate PSMs with razor IDs and description
Docker
docker pull prvst/philosopher:4.8.1
docker pull prvst/philosopher:latest
v4.8.0
1 year ago
Fixed
Fixed the protein coverage calculations with partially overlapping and subsumed peptides
Fixed an issue where peptides would map to multiple locations in the protein after having I/L converted (Needs to be used with MSFragger v3.6.1 or higher)
Fixed an issue with report tables having no isobaric labels being reported
v4.7.0
1 year ago
Added
Adjusted the peptide-to-protein mapping due to I/L replacement rules
Adjusted the protein FDR calculation rules.
Changed
Removed the normalization done at the protein level in label quant
Improved the protein filter for small scale analyses
Fixed
Adjusted the msstats file format, added purity to all plex sizes
Fixed the protein coverage calculations
Fixed repeated isobaric values that would eventually show up in the protein table
v4.6.0
1 year ago
Added
Added new flag --removecontam to the report command to remove contaminants from the reports
Added a new combined_psm report to abacus (beta)
Changed
Updated the TMT-Integrator to match with the version v4.0.0
Updated the pickedFDR filter
The pipeline command now accepts annotation files with prefixes
Updated PTMProphet to the latest release
Updated the database fetch with the new UniProt API (The new API is still unstable, people might experience hiccups with certain cases, especially non-model organisms without reviewed sequences)
Fixed
Contaminant tags are now added to Human sequences as well
Added a fix for errors causes by division-by-zero errors (PR by @chhh)
Fixed the protein coverage calculations to consider all peptides
Several minor fixes and updates
v4.4.0
1 year ago
Fixed
Issue with the database command only fetching the human FASTA.
Docker
docker pull prvst/philosopher:4.4.0
docker pull prvst/philosopher:latest
v4.3.0
1 year ago
Fixed
Updated the Endpoint from UniProt, fixing the database fetching issue.
Docker
docker pull prvst/philosopher:4.3.0
docker pull prvst/philosopher:latest
v4.2.2
1 year ago
Added
Decoys tag now appear inthe Gene and ProteinID
Support for TAIR database
Support for neXtProt database
Support for MSBooster scores which now appear in the PSM table
Fixed
Minor bugs andd issues were fixed
Docker
docker pull prvst/philosopher:4.2.2
docker pull prvst/philosopher:latest
v4.2.1
2 years ago
Added
Added support for TMT 18
Added option for contaminant tags in the database.
Changed
Added the parsing rules from the Prophets to the protein description.