- 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.
- 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.
- 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.
snap install philosopher
docker pull prvst/philosopher:2.0.0
docker pull prvst/philosopher:latest