MS resolution parameters¶
This panel feeds every downstream scoring step — resolving power, envelope crowding, and confounder search — regardless of which input path you use.
| Field | Default | Meaning |
|---|---|---|
| Resolving power R (at reference m/z) | 120,000 | The instrument's quoted resolving power at the reference m/z below — see Resolving power & FWHM |
| Reference m/z | 200 | Conventionally 200; the m/z at which the R value above was quoted |
| Safety margin (× FWHM) | 1.75 | Multiplier applied over the theoretical FWHM before calling a pair confidently (not just theoretically) separable |
| Ionization mode | Denatured | Denatured or Native — changes the charge-state ceiling model, see Charge-state envelopes |
Fragmentation scoring mode¶
Two mutually exclusive modes, radio-selected here:
- Calibrated (length-aware) — the primary, auditable formula. A single very long proteoform's own length can suppress every one of its bonds below the tier thresholds.
- RF ranking (no length) — for long proteoforms whose calibrated scores are all suppressed by their own length; a relative ranking within one proteoform, not a calibrated absolute score, and not comparable in magnitude to Calibrated mode's numbers.
See Fragmentation propensity & scoring modes for the full model, tier thresholds, and fold-enrichment numbers for both modes. Switching modes after running an analysis re-tiers and re-colors the whole MS2 ladder on the next Run analysis click.
Why this panel needs its own "Set"¶
Like MS strategy, this panel requires an explicit Set click before any analysis button unlocks — and re-locks itself if you change a value afterward. These parameters aren't previewed anywhere until you click Set; they take effect on the next analysis run, not retroactively on results already on screen.