search

compomics / psm_utils

Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
https://psm-utils.readthedocs.io
Apache License 2.0
24 stars 6 forks source link

fix parsing PSMs and complete protein names in XTandem #83

Closed julianu closed 2 months ago

julianu commented 4 months ago

[edited after adding fix for PSM parsing]

  1. As XTandem's protein names tend to be abbreviated in the protein "label" tag, change the origin to the "note" tag.

  2. While XTandem saves only the highest scoring PSMs per spectrum, these can still be more than one PSM, with different peptidoforms, if the score is exact the same. This is not an extremely rare case, especially with equal peptides (think of a single AA flip in the sequence). This fix parses the identifications with same peptidoforms into one new PSM, with only the relevant proteins assigned to each PSM. Before, there were weird matches of proteins to peptides, which did not occur in the databases used by XTandem.

  3. Also, it seems as the remark that only one protein per peptide/PSM is parsed is thus not true anymore.

julianu commented 4 months ago

I updated the comment for the initial PR, as there were some further additions to it.

codecov[bot] commented 2 months ago

Codecov Report

Attention: Patch coverage is 15.38462% with 11 lines in your changes missing coverage. Please review.

Project coverage is 63.97%. Comparing base (6e51896) to head (5d01b6f). Report is 2 commits behind head on main.

Files Patch % Lines
psm_utils/io/xtandem.py 15.38% 11 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #83 +/- ## ========================================== - Coverage 64.12% 63.97% -0.16% ========================================== Files 26 26 Lines 2492 2498 +6 ========================================== Hits 1598 1598 - Misses 894 900 +6 ``` | [Flag](https://app.codecov.io/gh/compomics/psm_utils/pull/83/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/compomics/psm_utils/pull/83/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics) | `63.97% <15.38%> (-0.16%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics#carryforward-flags-in-the-pull-request-comment) to find out more.

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.