Percolator "Picked protein FDR (-f)" option requires flanking amino acids in PIN peptide column

[tivdnbos]

see more at: https://github.com/percolator/percolator/wiki/Protein-inference-example

[RalfG]

I think you should already be able to do this with the percolator option in the configuration file:

{
    "$schema": "https://raw.githubusercontent.com/compomics/ms2rescore/master/ms2rescore/package_data/config_schema.json",
    "percolator": {
        "f": "path/to/sequence_db.fasta"
    }
}

or

{
    "$schema": "https://raw.githubusercontent.com/compomics/ms2rescore/master/ms2rescore/package_data/config_schema.json",
    "percolator": {
        "picked-protein": "path/to/sequence_db.fasta"
    }
}

See https://github.com/compomics/ms2rescore/blob/master/configuration.md.

Let me know if it works!

[tivdnbos]

It creates the following error message for the first PSM listed.

Exception caught: ERROR: Reading tab file, the peptide sequence with PSM id does not contain one or two of its flanking amino acids.

[tivdnbos]

FYI: If "tandem2pin" is used (not the one in rescore), the flanking amino acids do appear in the Peptide column ([flanking AA].[Peptide].[flanking AA]).

[RalfG]

Implemented for X!Tandem in #28, opened general issue: #27

[Hassan-1991]

Hi, has a solution for this been implemented in the MSGF+ms2rescore pipeline? I'm getting the exact error mentioned by tivdnbos above.