[t0mdavid-m]

Requested by Tom · project thread

Before: the Filtered PSMs page shows the annotated MS2 spectrum and the fragment coverage of the selected PSM. The per-ion evidence exists only as the *_fragment_ions.tsv export, with nothing in the app to look at it.

After: under the spectrum there is a new "Fragment ions" section for the selected PSM. It has a fragment mass error plot (m/z against error, in the fragment tolerance's unit from the Comet settings, with the ±tolerance band shaded, b ions in blue, y ions in orange, and dots sized by intensity) and a b/y ion table (theoretical m/z per position at charge 1+ and, for precursors with charge ≥3, 2+, with matched cells highlighted).

This is ProSE parity items P2 and P4.

How: src/common/fragment_plots.py reads only the selected PSM's rows from the run's fragment ion export with a lazy polars scan. It computes the theoretical b/y ions with pyOpenMS AASequence. Neutral-loss matches such as b4-H2O appear in the plot but don't mark a table cell. content/results_filtered.py reads the selection from the existing state manager and the tolerance from the workflow's params.json (CometAdapter-TMT in TMT mode).

This PR is independent of #42 and #43: it touches neither app.py nor the files those PRs change.

Validation: tests/test_fragment_plots.py adds 5 tests, and the full suite passes (124 tests). pylint --errors-only is clean. I also rendered the page in Chromium on a synthetic workspace.

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