Rosalind — Bioinformatics Stronghold — Mass spectrometry

SPEC — Inferring Protein from Spectrum

The answer is derived from the spectrum's consecutive differences (186.079 W, 131.040 M, 128.059 Q, 71.037 A) rather than restated from memory, and the assertion re-checks each residue against its own gap.

CONV — Comparing Spectra with the Spectral Convolution

solved Problem statement

Both spectra repeat a mass, so the winning difference (149.06586) arises four ways; the example prints that reasoning. The assertion also pins the three hand-checked occurrences of 85.03163 and the size of the convolution.

PRSM — Matching a Spectrum to a Protein

solved Problem statement

GSDMQS ties with IASMQS at multiplicity 3, so the assertion requires the reported protein to be one of the maximal ones rather than a single fixed string.

SGRA — Using the Spectrum Graph to Infer Peptides

solved Problem statement

Monoisotopic masses, so differences are matched within a tolerance rather than exactly. The graph is a DAG since masses only increase, so the longest path is one scan in sorted order instead of an exponential search.

FULL — Inferring Peptide from Full Spectrum

solved Problem statement

A peptide fragments from both ends at once, so a b-ion and its y-ion sum to the parent mass and the list mixes them unlabelled. It does not matter which is which — taking an ion spends its complement, since a prefix and its suffix are one event and cannot both extend the chain.