Computational and Statistical Methods for High-Throughput Mass Spectrometry-Based PTM Analysis

  • Veit SchwämmleEmail author
  • Marc Vaudel
Part of the Methods in Molecular Biology book series (MIMB, volume 1558)


Cell signaling and functions heavily rely on post-translational modifications (PTMs) of proteins. Their high-throughput characterization is thus of utmost interest for multiple biological and medical investigations. In combination with efficient enrichment methods, peptide mass spectrometry analysis allows the quantitative comparison of thousands of modified peptides over different conditions. However, the large and complex datasets produced pose multiple data interpretation challenges, ranging from spectral interpretation to statistical and multivariate analyses. Here, we present a typical workflow to interpret such data.

Key words

Proteomics Bioinformatics Post-translational modifications (PTMs) 



VS was funded by the Danish Council for Independent Research and the EU ELIXIR consortium (Danish ELIXIR node). This work was conducted as part of the EuPA Bioinformatics Community (EuBIC) initiative supported by the European Proteomics Association (EuPA).


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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Protein Research Group, Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdenseDenmark
  2. 2.Proteomics Unit, Department of BiomedicineUniversity of BergenBergenNorway

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