[t0mdavid-m]

Before: the PSM tables on Database Search, Rescoring and Filtered PSMs show the raw OpenMS string, e.g. .(Acetyl)M(Oxidation)DNFES(Phospho)TAEGNLSIGNK. The PSM downloads carry only that string as well.

After: a Modifications switch above each PSM table offers three views.

• Labels (default) shows ac-M(ox)DNFES(ph)TAEGNLSIGNK.
• ProForma shows [Acetyl]-M[Oxidation]DNFES[Phospho]TAEGNLSIGNK.
• OpenMS shows the original string.

The choice carries across the three pages and survives navigating away. Row selection still drives the spectrum and sequence views. The PSM and fragment-ion TSV exports gain a proforma column next to the OpenMS sequence.

This is ProSE parity item R10 (modification display switch).

How:

• src/common/peptide_format.py builds both forms with pyOpenMS AASequence, so any modification OpenMS knows works.
  • It uses Unimod names, with short labels for common ones (ox, ph, cam, ac, de, tmt, …).
  • Terminal mods are written as X- and -X.
  • A mod without a Unimod name falls back to its signed mass shift.
  • A string pyOpenMS can't read is shown unchanged.
• src/common/sequence_display.py handles the non-OpenMS views.
  • It reads the run's cached PSM table data and builds a second insight Table cache with the formatted Sequence column. The links, row ids, sort and columns are copied from the original's manifest.
  • That cache is built once per run and view, and replaced when a new run regenerates the base table.
  • Existing results get the switch without re-running the workflow.

Validation:

• tests/test_peptide_format.py has 8 tests: terminal mods, short labels, mass-only mods and pass-through.
• tests/test_sequence_display.py has 2 tests: the variant cache's data and manifest, and its rebuild after a new run.
• test_result_exports now checks the proforma column.
• pytest tests/ passed 123 tests.
• pylint --errors-only reports only the usual E0611 false positives on pyopenms imports (compiled module).
• I rendered Filtered PSMs in Chromium with acetyl, oxidation and phospho PSMs and switched through all three views. The OpenMS choice was still selected after going to Rescoring and back.

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