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

S Tyanova, T Temu, P Sinitcyn, A Carlson, MY Hein… - Nature …, 2016 - nature.com
S Tyanova, T Temu, P Sinitcyn, A Carlson, MY Hein, T Geiger, M Mann, J Cox
Nature methods, 2016nature.com
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 …
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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