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Oxford University Press, Nucleic Acids Research, W1(43), p. W326-W330, 2015

DOI: 10.1093/nar/gkv542

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MS2PIP prediction server: compute and visualize MS2 peak intensity predictions for CID and HCD fragmentation

Journal article published in 2015 by Sven Degroeve, Davy Maddelein, Lennart Martens
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

We present an MS2 peak intensity prediction server that computes MS2 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 MS2PIP model for Orbitrap-LTQ CID spectra. Predicted MS2 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 MS2PIP prediction server is accessible from http://iomics.ugent.be/ms2pip.