Philosopher 4.1.1

Fixed

• Fixed an issue with the ion mobility column not showing in empty PSM tables.
• Fixed an issue where high-scoring peptides mapping to complicated razor cases where not showing in the reports.

Docker images

• docker pull prvst/philosopher:latest

Philosopher 4.1.0

Added

• Support for TMTPro (18-plex)

Changed

• Decoys have NextAA and PrevAA
• Improved the filtering process

Fixed

• Fixed an issue with the labelling of the TMT-6 channels
• Minor bugs and issues

Docker images

• docker pull prvst/philosopher:latest

Philosopher 4.0.0

Added

• Native support for Thermo raw files (Windows, and Linux).
• Option to tag contaminant sequences with a prefix tag.
• New parameters added to MSFragger.
• Support for FAIMS data.
• New parameters for MSFragger.

Changed

• Improvements in overall performance.
• Improvements to the pipeline processing speed.
• Major code cleaning and refactoring.
• The pipeline protein inference is now calculated once for all data sets.
• Updated razor assingment classification.
• Upgated Go compiler to v1.16.5.

Fixed

• Label positioning in the reprint output.
• Minor bugs and fixes.
• Fixed problems with Spectral Counting.

Docker images

• docker pull prvst/philosopher:latest

Philosopher 3.4.13

Added

• Added support to compensation voltage.

Changed

• Tabular spaces in FASTA headers will be replaced by a simple space character.

Fixed

• Fix a bug that resulted in some peptides missing in the peptide report.

Docker images

• docker pull prvst/philosopher:3.4.13
• docker pull prvst/philosopher:latest

Philosopher 3.3.12

Added

• Fix to PTMProphet mod_nterm_mass change when using TMT-16 plex.

Changed

• Updated parallelization for PeptideProphet.
• Updated pipeline configuration file.
• When using a GENCODE database, the Gene name will now be the ENSG key from the header.

Fixed

• Fixed issue with an empty custom database.

Docker images

• docker pull prvst/philosopher:3.3.12
• docker pull prvst/philosopher:latest

Philosopher 3.3.11

Added

Changed

Fixed

• Fixed issue with an empty custom database.

Snapcraft

• snap install philosopher

Docker images

• docker pull prvst/philosopher:3.3.11
• docker pull prvst/philosopher:latest

Philosopher 3.3.10

Added

• A new Workspace option allows the use of a custom folder as a temporary folder.
• The Database now supports multiple database IDs (separate them with a comma).
• Support for the latest msconvert mzML format.
• Output prefix flag added to PTMProphet.

Changed

• The parameter file was updated, and the terms were made more human-readable.
• The code compilation is now done with GO v1.15.
• PTMProphet updated to v6.0
• The Abacus memory footprint as significantly reduced.

Fixed

• Small bugs and fixes.
• PSMs lists often contained observations mapping to proteins that did not pass the FDR filter.
• Bio quant was failing because of the unassigned database path.
• Some annotation files were being ignored.
• Added FASTA database file extension back again.

Snapcraft

• snap install philosopher

Docker images

• docker pull prvst/philosopher:3.3.10
• docker pull prvst/philosopher:latest

Philosopher 3.2.9

Added

Adding Zenodo DOI.

Fixed

Wrong assignment for the subFDR filtering.
PTMPRophet was having issues in replacing the PeptideProphet file.

Snapcraft

• snap install philosopher

Docker images

• docker pull prvst/philosopher:3.2.9
• docker pull prvst/philosopher:latest

Philosopher 3.2.7

Added

Changed

Fixed

• Issue with the label assignment in labelquant.

Docker images

• docker pull prvst/philosopher:3.2.7
• docker pull prvst/philosopher:latest

Philosopher 3.2.6

Added

Changed

Fixed

• Pipeline functions were restored.
• Ion Purity calculation was fixed, and now supports msconvert 3.20
• Fixed file discovery for filtering on Windows

Docker images

• docker pull prvst/philosopher:3.2.6
• docker pull prvst/philosopher:latest