Introduction

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.

Publications

  1. The Perseus computational platform for comprehensive analysis of (prote)omics data.
    Cite this
    Tyanova S, Temu T, Sinitcyn P, Carlson A, Hein MY, Geiger T, Mann M, Cox J, 2016-09-01 - Nature methods

Credits

  1. Stefka Tyanova
    Developer

    Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Germany

  2. Tikira Temu
    Developer

    Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Germany

  3. Pavel Sinitcyn
    Developer

    Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Germany

  4. Arthur Carlson
    Developer

    Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Germany

  5. Marco Y Hein
    Developer

    Cellular and Molecular Pharmacology, University of California, United States of America

  6. Tamar Geiger
    Developer

    Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Israel

  7. Matthias Mann
    Developer

    Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Germany

  8. Jürgen Cox
    Investigator

    Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Germany

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Summary
AccessionBT005659
Tool TypeApplication
Category
PlatformsWindows
TechnologiesC
User InterfaceTerminal Command Line
Download Count0
Country/RegionGermany
Submitted ByJürgen Cox