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Perseus is software package for shotgun proteomics data analyses, which helps to extract biologically meaningful information from processed raw files. It performs bioinformatic analyses of the output of MaxQuant, and thus completes the proteomics analysis pipeline. The software is implemented in a practical format consisting of a main core to which plugins are added. This allows easy integration of an unlimited number of independent statistical tools, which can thus be combined in an analysis. The software already includes various statistical methods and illustrations, such as data transformation, normalization and imputation, unsupervised and supervised learning methods, correlation profiling, enrichment tests, motif identification, volcano plots, scatter plots, and many many more. Additionally, it is possible to combine data from all omics sources for systems-wide analyses.

To run Perseus, you will need .NET framework 4.5. If you use Windows you should have Vista or newer. Like most Windows software, Perseus can also be run on a Mac. There is currently no support for linux, but it is on the horizon.

A note to internal users: Scientists at the Max Planck Institute of Biochemistry have access to Perseus features that have not yet been released to the public. To view the documentation of these features, you will have to log in using the button in the upper right corner of this page. If you do not yet have an account, you will need to register using the button next to the login button and then ask Art Carlson to add you to the internal group.

Documentation outline

This documentation is organized as a wiki, so if you find anything that is wrong or hard to understand, in most cases you can fix it yourself. The wiki can be browsed by using the links below or by searching with the box in the upper right. Anyone is allowed to read the wiki, but to make changes you will have to register and login using the button in the upper right.

For additional training, consider attending the annual MaxQuant Summer School. Also watching some MaxQuant videos provides more insight.

Comment: In the newest Perseus version we changed the terminology of expression columns to main columns. The functionality of these columns is equivalent.

Footnote on pronunciation.


perseus/start.txt · Last modified: 2016/09/22 13:40 by art