- Galaxy plugins, command-line tools, or Java library: It's up to you!
- Parse quantitative peptide information from tabular output (Progenesis and MaxQuant)
- Merge peptides based on alternative modifications (e.g. oxidation, acetylation), alternative tryptic digests, and charge states.
- Apply standard statistics (archsinh transform, ANOVA, t-test, fold-change, etc..).
- Export as a tabular or mzQuantML file
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