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Christian Panse, Jonas Grossmann, Bertran Gerrits, Ralph Schlapbach (Functional Genomics Center Zurich)Mass spectrometry (MS) is the method of choice for protein identification, quantification, and post translational modification assignment in proteomic studies. Due to the advent of accurate and fast sampling mass spectrometers, proteomic experiments often contain thousands of peptide fragmentation spectra. Although it is commonly accepted that no manual validation of individual spectra in such experiments is feasible, annotated spectra of the peptides assignments with their modifications are required for quality controle, publication, and reviewing purposes. Here we demonstrate a software application called peakplot that retrospectively computes ion tables and labels the spectra from a peptide sequence assignments by the Mascot search algorithm with the appropriate fragment ion labels. The application uses Perl for the manipulation of data and R for label heuristics and plotting. The standard output in PDF. peakplot greatly facilitates the visualisation of peptide fragmentation spectra and aides with the quality assessment of modification sites such as phosphorylation. web site: http://fgcz-peakplot.uzh.ch