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

Stefka Tyanova, Tikira Temu, Pavel Sinitcyn, Arthur Carlson, Marco Y. Hein, Tamar Geiger, Matthias Mann, Jürgen Cox*

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review


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 ( 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.

Original languageEnglish
Pages (from-to)731-740
Number of pages10
JournalNature Methods
Issue number9
StatePublished - 30 Aug 2016


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