Nesvilab/philosopher: 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 capabilities that will rely on the group passed by MSFragger.
• Support for sCLIP isobaric tags.

• Rolled back the FASTA header checking for IonQuant.
• Improved the FASTA header detection and parsing.
• PTMProphet was updated to v6.2.0.
• The processing speed, including IO operations and database reading received a major upgrade (@guoci).
• The purity column will always be visible in the PSM table.
• Updated the MSstats report for individual data sets.

• 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.