How do I run MaxQuant?

Double click on MaxQuant.exe in MaxQuant folder and specify your RAW files, experimental design and fasta files. Click on the Start button. We are supporting MaxQuant on Ubuntu 16 or higher, but MaxQuant should also work on another distribution of Linux. You may run MaxQuant using Graphical User Interface.

Is MaxQuant free?

MaxQuant is freely available and can be downloaded from this site. The download includes the search engine andromeda, which is integrated into MaxQuant as well as the viewer application for inspection of raw data and identification and quantification results.

What is label free mass spectrometry?

Label-free protein quantification is a mass spectrometry-based method for identifying and quantifying relative changes in two or more biological samples instead of using a stable isotope-containing compound to label proteins.

How do I add modifications to MaxQuant?

Adding a new modification You can visit http://www.unimod.org/ and select a modification that has not been defined yet in MaxQuant and add this modification to the modification list in MaxQuant.

What are razor peptides?

A razor peptide is a peptide that has been assigned to the Protein Group with the largest number of total peptide identified (IDs). If the razor peptide is also unique it only matches to this single Protein Group. If it is not unique, it will only be a razor peptide for the group with the largest number of peptide IDs.

What is label-free mass spectrometry?

How do I download and install MaxQuant?

If you need to, you can download the software and get installation instructions at the Microsoft Download Center. Double click on MaxQuant.exe in MaxQuant folder and specify your RAW files, experimental design and fasta files. Click on the Start button.

What is MaxQuant?

• MaxQuant is an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data. • MaxQuant detects peaks, isotope clusters and stable amino acid isotope-

What is MaxQuant and LabKey Server?

MaxQuant is open source proteomics software used to analyze mass spectrometry data. LabKey Server can import, analyze, and present this analysis data via the MaxQuant module.

How do I import TMT quantitation data from MaxQuant?

TMT quantitation data is automatically imported when present in the MaxQuant data. To see TMT results, click the (Details) link for the Protein Group of interest (hover over the first column to see the link). MaxQuant has TMT results in the following files, where X is the index of the “tag”, starting with 0: