Philosopher 3.2.5

Added

Changed

Fixed

• Pipeline functions were restored.

Docker images

• docker pull prvst/philosopher:3.2.5
• docker pull prvst/philosopher:latest

Philosopher 3.2.4

Added

• Added keepold flag for PTMProphet.

Changed

• Philosopher will ignore the interact file when interact.mod is present.
• Improved quantification mapping to all runs. The --mapmods option is only necessary to print mod reports.
• The number of tryptic ternmini is now determined by ProteinProphet.

Fixed

• Error preventing iTRAQ quantification.
• Several formatting, typoes and Go-Vet issues were fixed.

Docker images

• docker pull prvst/philosopher:3.2.4
• docker pull prvst/philosopher:latest

Philosopher 3.2.3

Fixed

• Loop error when trying to run Comet with the pipeline.

Snapcraft

• snap install philosopher

Docker images

• docker pull prvst/philosopher:3.2.3
• docker pull prvst/philosopher:latest

Philosopher 3.2.2

Added

• File Name added to PSM reports.
• New PeptideProphet parameter: --ignorechg can be used to ignore certain charge states.

Changed

• Updated to GO 1.14
• Philosopher wont stop when processing empty pep.xml files.

Fixed

• Error preventing iTRAQ quantification.

Snapcraft

• snap install philosopher

Docker images

• docker pull prvst/philosopher:3.2.2
• docker pull prvst/philosopher:latest

Philosopher 2.1.2

Added

• Added MGF writing and Decoy tags options to MSFragger.
• The Pipeline can now send Slack direct messages to users.

Changed

• Updated Slack API, direct messages can also ben sent now.

Fixed

• The Pipeline Filter command will now work without a protein inference.
• 2D filter is now reporting the approved sequences again.
• The mass Histogram amplitude was too wide.

Snapcraft

• snap install philosopher

Docker images

• docker pull prvst/philosopher:2.1.2
• docker pull prvst/philosopher:latest

Philosopher 2.1.1

Added

• Optional, faster alternative protein inference algorithm (not fully tested yet).
• Support for iTRAQ 4 and 8.

Changed

• Added deisotoping parameter to MSFragger section in the pipeline configuration file.
• Updated to support MSFragger 2.3 and TMT-Integrator 1.1.2

Fixed

• Generic FASTA parser is now checking the decoy status of all entries.
• Fixed minor issue with some unmodified peptides being marked as oxidized in some report files.
• Fixed how some terminal modifications were shown (due to capitalization).
• Fixed the sorting order of the headers in reprint.tsv files.
• FASTA protein report (writing a file containing the sequences of proteins passing 1% FDR) is back to the report command.
• Fixed typo in ProteinProbability in Abacus pipeline command.

Snapcraft

• snap install philosopher

Docker images

• docker pull prvst/philosopher:2.1.1
• docker pull prvst/philosopher:latest

Philosopher 2.0.0

Added

• Support for TMT-16 plex.
• Peptide FDR filtering to combined peptide reports in Abcaus.
• Support for our custom pepXML schema containing extra fields.
• Ion Mobility value added to PSM table.
• Number of Enzimatic Termini to PSM table.
• Number of Missed Cleavages to PSM table.
• Uncalibrated Calculated M/Z to PSM table.
• Uncalibrated Peptide Mass to PSM table.
• Mapped Genes to PSM table.
• Calibrated observed mass and m/z to PSM report.
• Philosopher will stop if an error is reported by the Prophets.

Changed

• Updated to Go v1.13.1.
• Updated Comet to version 2019011
• Removed RawMassDiff from the reports.
• The Delta Mass adjustment will only happen if there was no previous mass calibration during the search.
• The Corrected DeltaMass value is now used to map Unimod.
• Reports wont show isobaric labels that are not used for the analysis anymore (e.g. 10 TMT columns if only 8 are used).
• When processing empty pepXML, Philosopher will emit a warning, not a fatal error.
• Removed observed masses from combined peptide report.
• The nomenclature 'Experimental' and "Calculated' were replaced by 'Observed' and 'Calculated' on the PSM table.
• The Cluster command is now called Bioquant.
• Updated pipeline configuration file.
• Updated documentation.

Fixed

• The filter command was throwing an error when no protein data was present.
• Report with TMT was breaking when no annotation file was present.
• The Database command will throw an error if no input at all is provided.
• The Observed modifications masses were mapping outside the tolerance window.
• Wrong protein assignment in PSM tables
• The ions report had an issue with missing mapped proteins.
• Missing charge states from combined peptide report.
• Wrong assignment between PSMs and Ions in both reports.
• Missing observed masses from PSM report.
• Empty databases if ID was wrong.
• Minor bugs and issues.

Snapcraft

• snap install philosopher

Docker images

• docker pull prvst/philosopher:2.0.0
• docker pull prvst/philosopher:latest

Philosopher 1.5.1

Fixed

• An inconsistent error when trying to clean the workspaces with no data inside.
• The labelquant command was demanding the presence of an annotation file.

Snapcrat

• snap install philosopher

Docker images

• docker pull prvst/philosopher:1.5.1
• docker pull prvst/philosopher:latest

Philosopher 1.5.0

Added

• Added STATIC option to PTMProphet.
• Reprint option added to the yaml file.
• New Intensity-based Reprint report added to Abacus.

Changed

• Default PTMProphet EM value changed from 1 to 2.
• idconvert and msconvert are now unavailable.
• Abacus pepxml and protxml parameters dont require a value anymore.

Fixed

• Fixed a problem wih the PSM-to-Protein razor assingment.
• The error library API was fixed after a core update.
• Small bugs and performance improvement.

Snapcrat

• snap install philosopher

Docker images

• docker pull prvst/philosopher:1.5.0
• docker pull prvst/philosopher:latest

Philosopher 1.4.6

Fixed

• Fixed MSFragger setting when pritting correct tables.
• Fixed a small typo in the pipeline parameter file.
• Fixed path to the combined protein file when running the pipeline.

Snapcrat

• snap install philosopher

Docker images

• docker pull prvst/philosopher:1.4.6
• docker pull prvst/philosopher:latest