Table of Contents
How do I open a MaxQuant file?
The first of these is Raw files. Select that tab, then click “Load” to open a browser where you can select the file containing your raw data. You can select any number of files. You can also select all the raw data files in a single folder by using the “Load folder” button.
How does MaxQuant 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.
Is MaxQuant open source?
MaxQuant is open source proteomics software used to analyze mass spectrometry data.
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 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.
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 run MaxQuant on Windows?
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 Max Quant?
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.
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.
Is Perseus software free?
Downloading and using the software is free of charge.
How do I load data in Perseus?
1. Double click on the Perseus.exe file to execute the program; 2. In the main menu bar, open the Load menu and select the Generic upload; 3. Click on the Select button and browse the folder where your MaxQuant results were saved.
What does label-free detection Meaning?
Label-free detection (also label-free (LF) technology, label-free analysis or label-free sensing) uses optics-based biosensors to convert biological binding responses into signals without using a fluorescent or any other detection label.
How long does a Maxquant run take?
What are protein groups in Maxquant?
Protein groups
| Name | Description |
|---|---|
| Intensity L | Summed up eXtracted Ion Current (XIC) of the isotopic cluster linked to the light label partner. |
| Intensity M | Summed up eXtracted Ion Current (XIC) of the isotopic cluster linked to the medium label partner. |
How do you Analyse peptides?
In a traditional LC-MS/MS analysis of peptides, CAD is employed to dissociate small peptides derived from proteins by proteases, such as trypsin1,2. The peptide mixture is commonly separated by reverse-phase (RP) LC and introduced online into a mass spectrometer via electrospray ionization (ESI)3.
What is peptide intensity?
Peptide ion abundance is a sum of areas calculated using intensities of a given peptide ion’s constituent peaks as one of the inputs, the other one being those peaks’ width. The maximum intensity value is taken directly from a single point within the isotope boundaries.
What is Perseus software used for?
Perseus combines powerful machine learning and statistical methods for the classification of proteomics samples. For example, we have applied Perseus to study clinical classification of disease subtypes from proteomic data in lymphoma56, prostate cancer57 and breast cancer58 studies.
How do I import data from MaxQuant?
Select summary.txt and click Import Data. Choose Import MaxQuant Results and click Import in the pop-up. Return to your folder by clicking the MaxQuant Workspace link (your folder name will be shown) near the top of the page. In the Experiment Runs (Imported MaxQuant Results) web part, click the “Experiment Group” number, shown here as “1”.
What’s new in the MaxQuant version of the product?
The updated MaxQuant version has a map navigation component that steers the users through mass and retention time-dependent mass spectrometric signals. It can be used to monitor a peptide feature used in label-free quantification over many LC-MS runs and visualize it with advanced 3D graphic models.
How do I view my MaxQuant results?
View MaxQuant Results Return to your folder by clicking the MaxQuant Workspace link (your folder name will be shown) near the top of the page. In the Experiment Runs (Imported MaxQuant Results) web part, click the “Experiment Group” number, shown here as “1”.
Are the scan protocols compatible with the MaxQuant live?
Please note that every scan protocol has a version number, which is the version of the MaxQuant.Live that has been used to create or edit it the last time. Compatibility is not guaranteed if the scan protocols and the MaxQuant.Live ver- sion differ.