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Charge-state envelopes

Every MS1 chart in ProteoformTracker (the "MS1 charge-envelope overlay" in both Section 1 and Section 2) plots a predicted charge-state envelope for each proteoform — not a real acquired spectrum, since ProteoformTracker never touches raw instrument data. This page covers what's being predicted and how to read the chart.

Charge-state ceiling

Conditioned on the ionization mode you pick in MS resolution parameters:

  • Denatured, and roughly ≤ 40 kDa: the maximum charge state tracks the protein's own basic-residue count (Arg/Lys/His), since denaturing conditions let the charge ladder climb close to that ceiling.
  • Above ~40 kDa, or native mode generally: a Rayleigh-limit relationship tied to surface-area/mass takes over instead — native conditions in particular suppress charging well below the basic-residue ceiling.

Isotope pattern: resolved vs. unresolved

For each charge state, ProteoformTracker predicts the real isotope envelope shape (an Averagine closed-form approximation, not full combinatorial isotopologue enumeration — intractable at intact-protein scale) and then checks it against the instrument's own resolving power at that charge state's m/z (see Resolving power & FWHM):

  • Resolved (isotope spacing wider than the instrument's FWHM): drawn as a real discrete comb — one stick per actual isotope peak.
  • Unresolved (isotope spacing narrower than the FWHM — the common case above ~25–30 kDa, where the whole isotope envelope blurs into one hump): drawn as the smooth envelope curve those unresolved peaks would actually blur into.

Zoom into a single charge state's own narrow m/z window (scroll/pinch, or the +/− buttons) to see which regime you're in — the default zoomed-all-the-way-out view can't show individual isotope ticks even for well-resolved small proteins, since the full envelope spans hundreds to thousands of m/z.

Relative intensity, not absolute signal

The y-axis is normalized relative intensity, not a real absolute-intensity prediction — total ion signal divides across more charge states and a wider isotope envelope as mass increases, and ProteoformTracker models that redistribution, but absolute signal ultimately depends on sample loading and instrument sensitivity the tool has no way to know.

Hovering a peak

Once zoomed in enough (the hint text tells you when you haven't), hovering a resolved peak or an unresolved curve sample shows:

  • Its own m/z, charge state, and relative intensity
  • The nearest meaningful peak (≥1% relative intensity) belonging to a different proteoform in the same chart, and how many multiples of the instrument's FWHM apart they are — the same resolved/partially-separated/same-peak verdict language used everywhere else in the app

Where charge envelopes feed into scoring

  • MS1 stats tiles (clean/overlapping/total peaks): counts based on this same peak-collision check, run pairwise across every proteoform in the chart.
  • Confounder search: a candidate protein's own predicted envelope is what gets checked against your target's for the m/z-domain half of the search — see Relevant vs. confounding proteins.