Not able to run ms2resore through command line for this repo examples

[rolivella]

Hello

I'm trying to run ms2rescore through the command line with the example dataset available at the ms2rescore repo:

MGF file: https://github.com/compomics/ms2rescore/blob/master/examples/mgf/20161213_NGHF_DBJ_SA_Exp3A_HeLa_1ug_7min_15000_02.mgf.zip

MZID file: https://github.com/compomics/ms2rescore/blob/master/examples/id/msgfplus.mzid

And this config file: config.zip

If run it on Ubuntu 22.04 through this command: ms2rescore -c config.json -m 20161213_NGHF_DBJ_SA_Exp3A_HeLa_1ug_7min_15000_02.mgf msgfplus.mzid

I get this error. Am I missing some file? Thanks.

2023-07-04 14:37:49 // INFO // ms2rescore // Using MSGFPipeline.
2023-07-04 14:37:49 // INFO // ms2rescore.percolator // Running Percolator PIN converter

Pin-converter version 3.06.1, Build Date Jun 15 2023 14:57:04
Copyright (c) 2013 Lukas Käll. All rights reserved.
Written by Lukas Käll (lukas.kall@scilifelab.se) in the
School of Biotechnology at KTH - Royal Institute of Technology, Stockholm.
Issued command:
msgf2pin -P XXX -o /tmp/tmp3sn1zv2g/20161213_NGHF_DBJ_SA_Exp3A_HeLa_1ug_7min_15000_02_original.pin /home/proteomics/mysoftware/compomics/mgf/20161213_NGHF_DBJ_SA_Exp3A_HeLa_1ug_7min_15000_02.mzid

Uses features for fragment spectra mass errors
Reading /home/proteomics/mysoftware/compomics/mgf/20161213_NGHF_DBJ_SA_Exp3A_HeLa_1ug_7min_15000_02.mzid
No scan number was found for a PSM (or it equaled 0), scans are ranked from 1 and up
2023-07-04 14:38:01 // ERROR // ms2rescore.__main__ // Critical error occured in MS2ReScore
Traceback (most recent call last):
  File "/home/proteomics/.local/lib/python3.10/site-packages/ms2rescore/__main__.py", line 15, in main
    rescore.run()
  File "/home/proteomics/.local/lib/python3.10/site-packages/ms2rescore/__init__.py", line 233, in run
    peprec = self.pipeline.get_peprec()
  File "/home/proteomics/.local/lib/python3.10/site-packages/ms2rescore/id_file_parser.py", line 245, in get_peprec
    return self.peprec_from_pin()
  File "/home/proteomics/.local/lib/python3.10/site-packages/ms2rescore/id_file_parser.py", line 191, in peprec_from_pin
    raise IDFileParserError(
ms2rescore.id_file_parser.IDFileParserError: Could not map all MGF retention times to spectrum indices.

[rolivella]

Hello again, I've just reviewed my own issue and I'm a little closer to the solution. I understand from the documentation:

https://ms2rescore.readthedocs.io/en/latest/userguide/configuration/#mapping-psms-to-spectra

That I should add something like this to the JSON config file:

"spectrum_id_pattern": ".*scan=(\\d+)$",
"psm_id_pattern": ".*\\..*\\.(.*)"

However, in my mzid file there's no any spectrum_id field, so how can I parse the PSM with the psm_id_pattern?

Thanks!

[rolivella]

I modified the JSON config file with the correct regex and does not work:

• regex for the MGF file: https://regex101.com/r/VhBJRM/1
• regex for the mzID file: https://regex101.com/r/YWPevL/1

  "spectrum_id_pattern": ".*scan=(\\d+)$",
  "psm_id_pattern": "\\bscan=(\\d+)\\b"

Or:

    "spectrum_id_pattern": ".*scan=(\\d+)$",
    "psm_id_pattern": "mzspec.*scan=(\\d+)$"

[RalfG]

Hi @widmersimon,

Could you retry with MS²Rescore the latest beta version of MS²Rescore 3.0? You can install it with:

pip install ms2rescore --pre

Matching IDs from the PSM file to the spectrum files is always a bit tricky, as their is no single solution. We tried to streamline the process with v3.0.

Let us know if the issue persists and we'll gladly help you out!

[rolivella]

@RalfG thanks! I'll try it and let you know!

[rolivella]

@RalfG works like a charm! Thank you very much

[RalfG]

That's great to hear! Thank you so much for the update!