Interactive peptide spectral annotator: A versatile web-based tool for proteomic applications

Abstract

Here we present IPSA, an innovative web-based spectrum annotator that visualizes and characterizes peptide tandem mass spectra. A tool for the scientific community, IPSA can visualize peptides collected using a wide variety of experimental and instrumental configurations. Annotated spectra are customizable via a selection of interactive features and can be exported as editable scalable vector graphics to aid in the production of publicationquality figures. Single spectra can be analyzed through provided web forms, whereas data for multiple peptide spectral matches can be uploaded using the Proteomics Standards Initiative file formats mzTab, mzIdentML, and mzML. Alternatively, peptide identifications and spectral data can be provided using generic file formats. IPSA provides supports for annotating spectra collecting using negative-mode ionization and facilitates the characterization of experimental MS/MS performance through the optional export of fragment ion statistics from one to many peptide spectral matches. This resource is made freely accessible at http://interactivepeptidespectralannotator. com, whereas the source code and user guides are available at https://github.com/coongroup/IPSA for private hosting or custom implementations.