common¶

The same three-color scheme (plus a fourth, "neutral") appears in three different places in the app: exon blocks, MS2 fragment-ion ticks, and confounder-search fragment tiers. It always means the same thing: how many of the OTHER proteoforms currently being compared share this same element.

Color	Tier	Meaning
🟦 Blue `#2a78d6`	Unique	No other checked proteoform/confounder has this element — informative on its own.
🟪 Purple `#8952e0`	Partial	Shared with some but not all of the others.
🟨 Gold `#eda100`	Common	Shared with every other checked proteoform/confounder — not distinguishing.
⬜ Gray `#8a8a86`	Neutral	Nothing to compare against (only one proteoform checked).

Exon blocks¶

In the MS2 fragment-ladder track, each proteoform's exon structure is drawn as a row of colored blocks. An exon block is:

Unique if no other checked proteoform has that exact exon
Common if every other checked proteoform has it too
Partial otherwise

This is a real genomic-coordinate comparison (exact exon boundary match), not an axis-position heuristic.

MS2 fragment-ion ticks (b/y)¶

Each backbone bond's b-ion and y-ion tick is tiered by comparing its fragment mass against every other checked proteoform's (Section 1) or every currently-selected confounder's (Section 2) own fragment ladder, using the same resolving-power-derived mass tolerance used everywhere else in the app (see Resolving power & FWHM) — not a fixed Da cutoff.

Unique: this fragment mass matches nothing in any other ladder — if observed, it alone would distinguish this proteoform.
Common: every other ladder in the comparison also produces a fragment at this mass — this bond confirms nothing about which proteoform you're looking at.
Partial: matched by some, not all.

The per-proteoform unique/partial/common counts shown next to each row's title in the ladder are a live tally over only the bonds currently passing the fragment filter — they update immediately when you change the filter, so "how many informative fragments survive at the High-propensity threshold" is always a real, current number, not a static one computed once at analysis time.

Confounder-search tiers (Section 2)¶

Section 2 tiers the target's own ladder against whichever confounders you leave checked after selecting which to compare — so deselecting a confounder can promote some of the target's fragments from "common"/"partial" back up to "unique," since the tier is always relative to the current comparison set, not a fixed property of the fragment itself.