Basic-peptide depletion and precursor masking in bottom-up proteomics

Basic-peptide evidence is depleted in the basic isoelectric-point class versus their proteins’ theoretical tryptic precursors across 70,020 peptide-evidence rows (OR 0.45, 95% CI 0.44–0.46).

• Why it matters: Canonical protein identifications can rest on peptides with different properties, so proteoform-aware mapping is needed to quantify systematic biases in precursor-level evidence.
• What they did: The authors reanalyzed public bottom-up proteomics datasets using a proteoform-aware pipeline with a five-level confidence taxonomy, computed sequence-derived physicochemical features, and tested class-composition bias against digestion-matched backgrounds.
• The result: Depletion is absent for fully tryptic peptides (OR 1.06) and concentrates in missed-cleavage peptides (OR 0.62–0.57), with orthogonal validation showing basic-class odds ratio 0.73 (95% CI 0.71–0.76) and top-down span overlap of 90% but only 8% containment.

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