Breaking
- Completely new interface, one command (msstitch), some subcommands, merged several
functionalities (e.g. SQLite creation/output) into fewer steps.
Added
- Possible to add ion mobility value of scans to PSM table
Changed
- Updated README
- Output column name changes (esp Gene ID/ Gene name from symbols)
- peptide sequence in first column of peptide table output
- trypsinize adds peptide index to fasta output as to not create duplicate entries
- PSM table creator does not longer take a mapfn from biomart, all info comes from fasta header
- Consequently, picked FDR can now work on ENSG ID and gene names
- SQLite creation for spectra has possiblity to specify output file
- Percolator output splitprotein different behaviour: can specify "known" prot headers which excludes all scans with those annotations,
when not specified it keeps any scan for a header (also if other headers are specified)
Fixed
- msslookup quant no longer stores duplicates if >500.000 scans, those first 500.000 were stored twice
Removed
- percolator split/merge/filter/qvality scoring, only kept protein identity splitting
- Protein error probability output