glormph
commented
1 year ago It is possibly this: A peptide AAATPESQEPQAK in a search (sars etc normtotal), has a phospho on T4 and S7. In the PTM peptide table, the S7 is NA in set1-3, but not in set4. In the normal peptide table the same S7 PTM has q-values in all sets. I am not 100% yet, since I didnt do a full re-run, but:
The PTM PSM table has only support in set4 for S7-P. In the normal PSM table, the same scans have T4-P instead. That probably means, that the luciphor saw those PSMs, and decided that the PTM is on the wrong residue there (FLR is quite good in the PTM table). We then generate from the PTM PSM table a peptide table, but here we take the "peptide" which is called AATPESQEPQAK_Phospho:T4 instead of the MSGF-reported sequence as the sequence. Since there are no such peptides (after luciphor) for e.g. set1, the ones in set1-3 are set to NA.
To be completely sure I'll have to rerun the luciphor process.
Sometimes a peptide has NA for isobaric quant in a set for PTM peptides, but not in the peptide table. This may be a bug, or just unclear.
Also, doc how collapsing of two identical-seq, identical PTM peptides work for PTM table, if two molecules are found with e.g. different oxidation.
Please check and document. For @harbab