FAQ & troubleshooting

"Run analysis" / "Load isoforms" is greyed out

Both the MS strategy and MS resolution parameters panels need their own Set button clicked at least once — every entry-point button (Load isoforms, Run sequence analysis, Find matching transcripts, Run analysis) stays disabled until both are set. This isn't a bug: it's a deliberate confirmation step for settings everything downstream depends on. Changing a value in either panel after clicking Set re-locks it, requiring a fresh click.

For "Run analysis" specifically, you also need: at least one proteoform checked/selected, and a confounder-search target picked in the dropdown.

The confounder search only found a few results — is that right?

It depends entirely on found_via. A target with few real mass-domain neighbors and few m/z collisions genuinely can have a short candidate list — that's a real result, not a bug. Check the status line's "N by mass window, N by m/z collision, N by both" breakdown; see Relevant vs. confounding proteins.

My confounder list is capped at 30 — how do I see more?

By design, for performance — see why the list is capped. The status line reports the true total found. There's currently no way to raise the cap from the UI.

The MS2 ladder shows nothing for a bond I clicked

The fragment-isotope inspector only computes for bonds whose propensity score clears the current scoring mode's isotope gate (Calibrated: score > 0.10; RF: score > 0.08). If you click a bond below that gate, the label explains this rather than showing an empty chart — try the Elevated filter level to only click bonds that will actually qualify.

GLM ("Calibrated") mode shows almost nothing above the "Elevated" filter for my protein

This is the expected behavior the RF mode exists to fix — a single very long proteoform's own length systematically suppresses its calibrated score. Switch Fragmentation scoring mode to RF ranking in MS resolution parameters; see Fragmentation propensity & scoring modes for why the two modes aren't on the same numeric scale.

Reset doesn't seem to clear everything

If you hit this on an older build: newer versions explicitly tear down chart interaction listeners and re-collapse both result sections on Reset, so nothing from a previous analysis can reappear (e.g. via a stray scroll over a chart area). If you still see stale content after Reset on a current build, that's worth reporting as a real bug.

FASTA / rMATS input tabs say alignment isn't available

These need a local GRCh38 genome FASTA + minimap2 index, which isn't required for Option 1 and is gitignored (not shipped with the repo). See Installation & setup.

Where do I report a real bug?

Open an issue on the app repository.