What is MaxQuant?

MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high-resolution mass spectrometry (MS) data. Currently, Thermo LTQ-Orbitrap and LTQ-FT-ICR instruments are supported and Mascot is used as a search engine.

Is MaxQuant open source?

MaxQuant is open source proteomics software used to analyze mass spectrometry data.

What is a label-free methods?

Label-free quantification is a method in MS that determines the relative amount of proteins in two or more biological samples, but unlike other quantitative methods, is does not use a stable isotope that chemically binds and labels the protein.

What is label-free?

Label-free means that you don’t have to tag your molecule of interest with any tag to SEE it, (like in ELISA or RIA), you detect the binding to your biosensor because of its linking properties with the biosensor itself.

How long does a MaxQuant search take?

Computation times : Processing time is currently about 20 min per raw file and per processing core.. Typical values for 72 LC/MS runs are 16 h.

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.

How does Max Quant work?

The MaxQuant suite is a set of algorithms, which includes peak detection and scoring of peptides, it performs mass calibration and database searches for protein identification, it quantifies identified proteins, and provides summary statistics.

What is the name of the search engine that MaxQuant has?

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. For statistical analysis of MaxQuant output, we offer the Perseus framework.

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 Lfq proteomics?

Relative label-free quantification (LFQ) of shotgun proteomics data using precursor (MS1) signal intensities is one of the most commonly used applications to comprehensively and globally quantify proteins across biological samples and conditions.