What is MaxQuant used for?

MaxQuant is a quantitative proteomics software package designed for analyzing large-scale mass-spectrometric data sets. It supports all main labeling techniques like SILAC, Di-methyl, TMT and iTRAQ as well as label-free quantification.

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 is an Andromeda score?

The Andromeda score is calculated as −10 times the logarithm of the probability of matching at least k out of the n theoretical masses by chance as shown in Figure 3. This is slightly different from Olsen et al., (48) where the probability of matching exactly k out of n theoretical masses is determined.

What is MaxQuant software?

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.

How long does MaxQuant take to run?

Hi, it depends on your workstation that you are using to do your analysis. It varies for me for a day or two on the basis of computer I have used. My laptop (8 GB RAM) takes around 2 days to give back the output of 7 such raw files, while the another PC at lab (16 GB) takes less than day to process it.

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.

What is a 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. If it is not unique, it will only be a razor peptide for the group with the largest number of peptide IDs.

How do I install MSstats?

Installing MSstats as an External Tool o On the “Tools” menu, click “External Tools” to bring up the External Tools form. o Click the “Add…” button, and select “From Tools Store…” from the menu that appears. o Navigate to the “MSstats” tool to see the installation status and a description. o Click Install.

How can I speed up my MaxQuant?

You can increase the number of processors or threads (depending upon the MaxQuant version you re using) to speed up the MaxQuant processing. In general, one thread needs 2GB of RAM for processing, so if your computer has 8GB RAM, you can increase the number of processors to 4.

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.

What is Lfq intensity?

LFQ (label-free quantitation) intensity is a very similar to the iBAQ intensity but the protein intensities are normalized to exculde some “outliers” to best represent the ratio changes of different samples. Mass spectrometer generated raw files are used for label-free quantitation of proteins.