title: MS2PIP prediction server: compute and visualize MS2 peak intensity predictions for CID and HCD fragmentation.
abstract: We present an MS(2) peak intensity prediction server that computes MS(2) charge 2+ and 3+ spectra from peptide sequences for the most common fragment ions. The server integrates the Unimod public domain post-translational modification database for modified peptides. The prediction model is an improvement of the previously published MS(2)PIP model for Orbitrap-LTQ CID spectra. Predicted MS(2) spectra can be downloaded as a spectrum file and can be visualized in the browser for comparisons with observations. In addition, we added prediction models for HCD fragmentation (Q-Exactive Orbitrap) and show that these models compute accurate intensity predictions on par with CID performance. We also show that training prediction models for CID and HCD separately improves the accuracy for each fragmentation method. The MS(2)PIP prediction server is accessible from http://iomics.ugent.be/ms2pip.
authors.affiliation: Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent, Belgium Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium sven.degroeve@vib-ugent.be.
authors.forename: Sven
authors.initials: S
authors.lastname: Degroeve
authors.affiliation: Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent, Belgium Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium.
authors.forename: Davy
authors.initials: D
authors.lastname: Maddelein
authors.affiliation: Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent, Belgium Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium.
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
mesh_terms: D020407:Internet; D010455:Peptides / Q000737:chemistry*; D040901:Proteomics / Q000379:methods; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010455:Peptides