MaxQuant is a suite of algorithms for analysis of high-resolution mass spectrometry (Orbitrap and FT) data. It can be used for protein identification and intensity-based label-free quantification for non-labeled samples and identification and quantification for SILAC-labeled, or TMT-labeled or iTRAQ-labeled samples. MaxQuant includes all steps needed in a computational proteomic platform. It uses its own Andromeda search algorithm for peptide identification. In brief, in a seamless workflow, raw data acquired on Orbitrap, is processed using MaxQuant’s “Quant” module. The processed data is further searched with Andromeda. Eventually, the Andromeda search output files are subjected to statistic analysis and protein grouping using the “Identify” module.

To run this software under Windows, connect using instructions provided on our Windows systems page. Once logged in, navigate to

Start > All Programs > MaxQuant

Users should make a copy of the software if they wish to make modifications to MaxQuant configuration. This can be done by right clicking the folder in the start menu, choosing Copy, and then pasting the files to e.g. the U drive, S drive or G drive (be sure to review relevant storage policies to prevent data loss). Note also that MaxQuant can be freely downloaded from and does not require administrative privileges to use.

For use of latest version, users are recommended to join the MaxQuant google group at the following website. Please send an email to in case you have any questions regarding the usage of this version.

For version, users are requested to follow instructions on using MaxQuant as shown in the following pdf file (prepared by Rich Beck).

For use of version, please refer to the following webinars:

          Introduction to MaxQuant:

          How to use MaxQuant:

Videos for use of MaxQuant and Perseus can be found at MaxQuant youtube channel:

For transferring data onto MSI Windows systems, your group might require a folder that can be used to transfer your data from project space for MaxQuant analysis. Please send a mail to if you need project space for your group.

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