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Philosopher 2.0.0
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@prvst prvst released this 08 Nov 21:56
· 1795 commits to master since this release
v2.0.0
16c007e
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Learn about vigilant mode.

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
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