Msstitch

Fixed
- MS1 alignment had a 60x too large retention time window (minutes instead of seconds)

Changed
- Wording "amount" to "count" or "total number"
- Protein FDR can be picked or classic with a command line parameter

Fixed
- PEP/q-value field positions in PSM table
- Allow whitespace at end of TSV line

Added
- Add PEP (posterior error) from percolator to output
- Possible to do median-centering on a peptide/protein/gene table using median factors from another table (e.g. PTM peptides centered with a protein table)

Changed
- No longer recalculate percolator FDR to avoid mix-max, let user choose in percolator instead

Fixed
- Genecentric peptide table merging bug with many identical gene output fixed

Changed
- Field order in peptide/protein tables: channels of all sets, then of PSMs used to quantify

Fixed
- Deletesets bug where unused peptide sequences where not removed from DB due to a missing commit
- Fix percolator to TSV ID creation which affected non-scannumbered data (e.g. TIMS data) where multiple PSMs to spectrum occur and it keeps enumerating scans

Fixed
- Peptide table merge bug that piled on duplicate proteins and exploded in processing time at big datasets

Added
- Total protein normalization of PTM peptides
- PTM FLR stored and output in peptide table merges
- Precursor ion fraction (purity) from OpenMS to PSM table
- Precursor purity filter sets PSM quant to NA, keeps PSMs

Fixed
- Do not create duplicate isobaric channels in DB and with that in PSM output
- Do not add standard fields to PSM refined header that are already there
- Do not crash on peptide table merge when a peptide has e.g. 600 protein matches
- Merging no-group peptide tables no longer output multiple identical protein accessions for a peptide
- Peptide table genecentric merge gets all genes per peptide, not only one