Family-member protein reads + Percolator .target.pop guidance - #4
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Family-member protein reads + Percolator .target.pop guidance#4lostculture wants to merge 1 commit into
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ms_peptidesummary.getHit() returns only protein-family representatives, so homologous proteins clustered as family members are silently missed. Add a section on walking family members (getNextFamilyProtein / getHitAndFamilyMember), plus how to import Percolator results from the cache .target.pop (not in the SQLite .msr) and a .target.pop-driven reader recipe. Correct sqlite-msr.md to note SQLite lacks Percolator q-values and clustering. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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ms_peptidesummary.getHit() returns only protein-family representatives, so homologous proteins that cluster as family members are silently missed. This adds:
Surfaced while reanalysing a published 2D-TPP dataset: three validated chemoreceptor hits were 'missing' purely because they're family members under a 38-protein homolog cluster.
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