msgfplus rescoring support or AlphaPeptDeep format example

[gsaxena888]

I'd like to use the output of the msgfplus search engine (which I can convert to percolator format) as an input toAlphaPeptDeep's rescoring module. However, I don't think that either msgfplus output or percolator output is supported? Thoughts?

(One idea I had was to write a converter from msgfplus (or percolator) to the "AlphaPeptDeep" format, but I couldn't find an example file for AlphaPeptDeep and documentation for what fields are required so that I could create such a converter. Thoughts?)

[jalew188]

Do you have an example of the msfg+ format you would like to use? I am happy to help. The readers were in alphabase (https://github.com/MannLabs/alphabase/tree/main/alphabase/psm_reader and https://github.com/MannLabs/alphabase/blob/main/alphabase/constants/const_files/psm_reader.yaml)

[gsaxena888]

Here's an mzid file I generated from an msgfplus search.(It's small, as it corresponds to peptides identified in a small 4Th precursor window.) (I couldn't generate the Percolator pin file -- the normal msgf2pin converter failed with some memory pointer error.) cyto_62_min2subsumed.mzid.gz

[jalew188]

does pyteomics support this mzid file?

[jalew188]

Close this issue as there are no activities for a long time