Philosopher 5.1.0

Added

• 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

• 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

Philosopher 5.0.0

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.

Philosopher 4.8.1

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

Philosopher 4.8.0

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

Philosopher 4.7.0

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

Philosopher 4.6.0

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

Philosopher 4.4.0

Fixed

• Issue with the database command only fetching the human FASTA.

Docker

• docker pull prvst/philosopher:4.4.0
• docker pull prvst/philosopher:latest

Philosopher 4.3.0

Fixed

• Updated the Endpoint from UniProt, fixing the database fetching issue.

Docker

• docker pull prvst/philosopher:4.3.0
• docker pull prvst/philosopher:latest

Philosopher 4.2.2

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

Philosopher 4.2.1

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.
• Removed RawReader.
• Improved processing speed and resource usage.
• Reduced binary size.

Fixed

• Several bugs and code fixes added.
• Fixed issue with TMT 6 plex quantification.

Docker

• docker pull prvst/philosopher:4.2.1
• docker pull prvst/philosopher:latest