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      The Perseus computational platform for comprehensive analysis of (prote)omics data.

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          Abstract

          A main bottleneck in proteomics is the downstream biological analysis of highly multivariate quantitative protein abundance data generated using mass-spectrometry-based analysis. We developed the Perseus software platform (http://www.perseus-framework.org) to support biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. Perseus contains a comprehensive portfolio of statistical tools for high-dimensional omics data analysis covering normalization, pattern recognition, time-series analysis, cross-omics comparisons and multiple-hypothesis testing. A machine learning module supports the classification and validation of patient groups for diagnosis and prognosis, and it also detects predictive protein signatures. Central to Perseus is a user-friendly, interactive workflow environment that provides complete documentation of computational methods used in a publication. All activities in Perseus are realized as plugins, and users can extend the software by programming their own, which can be shared through a plugin store. We anticipate that Perseus's arsenal of algorithms and its intuitive usability will empower interdisciplinary analysis of complex large data sets.

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          Author and article information

          Journal
          Nat. Methods
          Nature methods
          1548-7105
          1548-7091
          Sep 2016
          : 13
          : 9
          Affiliations
          [1 ] Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
          [2 ] Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA.
          [3 ] Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
          [4 ] Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
          Article
          nmeth.3901
          10.1038/nmeth.3901
          27348712
          119e342a-dc54-47f7-8984-f78c56296862

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