feat: ProForma 2.0 reader/writer and Layer-2 modification converter#1072

Open

trishorts wants to merge 25 commits into

smith-chem-wisc:masterfrom

trishorts:feature/proforma-reader-writer

Commits on May 24, 2026

test(proforma): add manuscript-example corpus and loader scaffolding

trishorts
and
claude
committed
feat(proforma): wrap TopDownProteomics in a Readers/ProForma facade

trishorts
and
claude
committed
test(proforma): map SDK Layer-1 coverage across full corpus

trishorts
and
claude
committed
feat(proforma): add Layer-2 ProFormaConverter for per-residue mods

trishorts
and
claude
committed
feat(proforma): resolve UNIMOD/MOD/RESID accessions in Layer-2 converter

trishorts
and
claude
committed
feat(proforma): resolve N-/C-terminal mods in Layer-2 converter

trishorts
and
claude
committed
test(proforma): validate Layer-2 converter against real Unimod database

trishorts
and
claude
committed
feat(proforma): add IBioPolymerWithSetMods.ToProFormaString bridge

trishorts
and
claude
committed
feat(proforma): add ProForma psmtsv output column header

trishorts
and
claude
committed
feat(proforma): parse the ProForma psmtsv column on read

trishorts
and
claude
committed

Commits on May 25, 2026

Commits on Jul 11, 2026

Commits on Jul 14, 2026

feat(ProForma): register ProForma as a SequenceConversion format

trishorts
authored and
trishorts
committed
test(ProForma): lift PR patch coverage 74.8% -> 91.8%

trishorts
authored and
trishorts
committed
Merge branch 'master' into feature/proforma-reader-writer
trishorts
authored