Pushed to glormph/adapt
c6e281d Need a empty protein table for e.g. decoy proteins
a720298 Added tool XML for protein table qvality runs
e00c957 Added tool to create protein table from just precursor peptide quantifications. Also edited msstitch py wrapper to enable this and coming qvality stuff.
b61a189 Added ms1 quant and protein probability tool xml files
cb1c941 Msstitch got a lot of updates, complying
2d1fdab Fixes for adding protein data to a single protein table
7efe5de Build mslookup db of protein tables also includes protein probability
78b542a Add protein probability to protein table supported in msstitch.py wrapper
3a45047 Merged protein table from multiple protein tables can optionally include precursor and/or isobaric data
a7f188f Peptide table building changes in tool xml
dcf3e68 Adding MS1 quant to protein table from PSM table
e1aa0a7 Bugs in storing precursor quants to db
3d718bd Filtering percolator sequences from sqlite got small makeover. Now can deliver own prepared trypsinized db.
5471984 remove print statement
e7bc7b3 Creating percolator metafiles now works with experimental data instead of setting a batch size on the tool. More flexible for users.
7e11651 Richer experiment data and corresponding lots of changes in how tools handle it. Makes linking spectra everywhere unneccessary.
6984ac2 Typo in tool xml
d2cf768 Possibility to add PSM amounts to protein quant table
3a1140d PSM quanting changed a lot in msstitch
3cfc4d1 Adding protein groups to PSM table changed a little bit
65444bd New protein group lookup tool XML
ddb98fa Also XML tool file for PSM lookup
97fdf3e Not alphabet sorting when merging percolator files per sample pool/biological set. Instead, lookup task nrs via mzML sets.
7ca22b9 Added peptide table maker tool
df4ff5e Sort input files to percolator correctly, after tasknr.
1cefe97 Split mzmlfiles into job workdirs and get their real name instead of dataset_x.dat
2211a80 Adapting pout2mzid to multi-pool/set FDR calculation. Previously took 1 percolator file, now takes files of different pools