How do I run MaxQuant?

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 open source?

MaxQuant is freeware, and contributions to new functionality are collaboration-based. The code of open source parts is available at https://github.com/JurgenCox/compbio-base.

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 proteomics?

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.

What is iBAQ?

The iBAQ corresponds to the sum of all the peptides intensities divided by the number of observable peptides of a protein. Each of these methods has been described as a valuable tool to estimate protein abundance and to compare the relative quantities of proteins [32].

What is a razor peptide?

What is Razor peptide? 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.

What is label-free analysis?

What is extracted ion chromatogram?

Extracted ion chromatogram (EIC) is created by plotting the intensity of the signal observed at chosen mass-to-charge value or series of values in a series of mass spectra recorded as a function of retention time.

How is iBAQ calculated?

The iBAQ value is obtained by dividing protein intensities by the number of theoretically observable tryptic peptides between 6 and 30 amino acids29, and is on average highly correlated with protein abundance29,39.

What is a unique peptide?

A unique peptide is defined as a peptide, irrespective of its length, that exists only in one protein of a proteome of interest, despite the fact that this peptide may appear more than once in the same protein.

What is label-free proteomic analysis?

3.7. 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 spectral count?

Spectral count, defined as the total number of spectra identified for a protein, has gained acceptance as a practical, label-free, semiquantitative measure of protein abundance in proteomic studies. The use of spectral counting for different types of quantitation studies is explored and critiqued.

How to run MaxQuant on a Linux instance?

You can manage your MaxQuant versions however you like, just make sure that it’s reflected in the gen_mqpar.py script. Move your protein FASTA files over to the Linux instance. The current gen_mqpar.py script has the path to the FASTA file hard-coded, and it’s straightforward to change this or make it argument-driven.

What kind of processor is used in MaxQuant?

We analyzed 300 LC-MS runs with MaxQuant using 120 logical cores in parallel, once with Ubuntu Linux (version 16.04.3) and once with Windows server 2012 R2 as the operating system. We used identical hardware in both cases: four Intel Xeon E7-4870 CPUs and 256 GB of DDR3 RAM.

How to install GCC8 for MaxQuant in Linux?

You can install gcc8 with these commands: (Thanks to @cscaife for identifying this step, and https://stackoverflow.com/a/55876012 for the install instructions) Create template mqpar.xml files – representing configurations for MaxQuant searches you routinely run on your experiments.

How to create MaxQuant configuration files in console?

The goal of the gen_mqpar.py script is to create MaxQuant configuration files ( mqpar.xml files) in a console environment without having to transfer one over or edit the XML manually. The example given has some hard-coded stuff and makes assumptions about your filesystem, so please follow the steps below to get started.