Measuring the abundance of proteins is a crucial part of most proteomics experiments and TPP provides several different tools for quantitation based on the experimental workflow, label-free, isobaric labeling, or isotopic labeling. The StPeter tool is designed for label-free datasets. It reads as input a protXML file as well as the corresponding pepXML and mzML files, deriving abundance measurements based on quantitation of the most abundant identified peaks in the MS2 spectra. PSM, peptidoform, and peptide abundances are rolled up to proteinlevel metrics using the SIn approach and written to protXML for further use. The StPeter2Matrix tool takes a series of protXML files from different samples and produces a quantitation matrix where each column is a sample.