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ProteoformTracker

ProteoformTracker

ProteoformTracker is an online web tool for isoform/proteoform-level detectability in top-down and middle-down proteomics (TDP/MDP). It answers one specific question:

Given a specific proteoform, can this instrument actually tell it apart from background proteoforms?

It's designed for users who already have candidate target protein isoforms — identified via RNA-seq-based alternative-splicing analysis (short-read/NGS or long-read sequencing) and/or literature-guided PTMs — and who plan to use TDP/MDP to identify these specific protein isoforms.

ProteoformTracker is a companion project to IsoPepTracker (its bottom-up counterpart).

What it does

  • Takes a proteoform from one of three input formats — a gene's annotated isoforms, a pasted/uploaded FASTA sequence (corresponding to de novo assembled transcripts or long-read sequencing results), or an rMATS alternative-splicing event — and resolves it into a shared internal representation (sequence + PTMs).
  • Predicts each proteoform's MS1 charge-state envelope (with real isotope patterns where the instrument would resolve them) and scores whether it's cleanly separable from every other checked proteoform, using an Orbitrap resolving-power model.
  • Generates each proteoform's MS2 b/y fragment ladder, scores each bond's fragmentation propensity, and classifies every fragment as unique / partial / common relative to the other checked proteoforms — so you can see exactly which peaks would actually distinguish two isoforms.
  • Searches the full reference human proteome for confounding proteins — unrelated proteins that could share your target's intact mass or a charge-state m/z peak — and lets you compare against a user-curated subset of them.
  • Supports middle-down workflows (simulated partial protease digestion) as well as intact top-down analysis.

Where to start

Source