Input Output GUI Synopsis Analysis Tools reSpect pepXML, mzML mzML Y Writes out new mzML files wherein the chimeric spectra with confident peptide identifications have had their MS2 peaks for those peptides subtracted to leave behind the peaks of co-eluting precursors, which may be re-subjected to searching to identify these co-eluting precursors. . Overview of many of the more minor TPP tools not described elsewhere in the article, along with their input formats, output formats, whether they are accessible with the GUI (or only the command-line), and a brief description.