nx_peptide_msms.nx

nx_peptide_msms.nx -- SOTA ANALYTICAL CAPSTONE: peptide identification by MS/MS spectral matching. Given an observed fragment-ion peak list, it generates the theoretical b/y ladder for a candidate sequence, matches observed against theoretical within a tolerance, and returns an identity score, the sequence coverage, and -- across a set of candidates -- which peptide the spectrum IS. This is the literal core of how a mass spectrometer identifies a peptide. WHY IT IS STATE OF THE ART. A single-mass match ("a peak near 1046") is a guess; a fragment-spectrum match is an identification. Backbone cleavage gives the b (N-terminal) and y (C-terminal) ion ladders, and a real ID scores how much of that predicted ladder the instrument actually saw, and how much of the backbone that covers. That is what nx_peptide_msms computes. ANCHORED, NOT ASSERTED. The b/y ion masses come from the residue table that two independent methods (residue-sum and elemental formula) agree on and that matches published values; the scoring is exact integer arithmetic. The gate liar-kills it: a spectrum matched against its OWN sequence scores a perfect 1000, and against a DIFFERENT peptide scores low -- if the matcher could not tell them apart it would be useless, and the negative control proves it can. The b_i + y_(n-i) = M + 2*proton invariant (proven in nx_peptide) means the two ladders are not independent evidence of the same thing twice; coverage counts a backbone SITE as seen if EITHER its b or its complementary y ion appears, which is the honest way to score. All INTEGER, _q4 = x10^4 Da matching nx_peptide. Grounding (cited; researcher-groundable): biemann_1990_peptide_fragment_ion_nomenclature eng_1994_sequest_cross_correlation_spectral_match published_peptide_ms_ms_fragment_ladders genealogy_id: peptide_chemistry + analytical_sota + liar_killer