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Protocols

MaxQuant specifications

Information


Unique identifier OMICS_02463
Name MaxQuant
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Windows
Computer skills Medium
Stability Stable
Maintained Yes

Subtool


  • MaxLFQ

Versioning


No version available

Maintainer


  • person_outline Juergen Cox

Publications for MaxQuant

library_books

MaxQuant goes Linux.

2018 Nat Methods
PMID: 29855570
DOI: 10.1038/s41592-018-0018-y

MaxQuant citations

 (2083)
library_books

Evolutionary instability of CUG Leu in the genetic code of budding yeasts

2018
Nat Commun
PMCID: 5951914
PMID: 29760453
DOI: 10.1038/s41467-018-04374-7

[…] fingerprinting rather than complete de novo peptide sequences, we generated 19 hypothetical proteome databases from each genome, corresponding to every possible sense translation of CUG. We then used MaxQuant, version 1.5.5.1 to identify peptides that had a unique match to only one of these databases, filtered the matches to include only CUG-encoded residues that were individually supported by b- […]

library_books

Comprehensive proteome analysis of nasal lavage samples after controlled exposure to welding nanoparticles shows an induced acute phase and a nuclear receptor, LXR/RXR, activation that influence the status of the extracellular matrix

2018
PMCID: 5946400
PMID: 29760600
DOI: 10.1186/s12014-018-9196-y

[…] on method utilizing collision-induced dissociation for sequencing on an LTQ Velos Orbitrap Pro mass spectrometer (Thermo Scientific). Identification and relative quantification was performed with the MAXQuant software against a human database downloaded from Uniprot (October 31, 2015). Protein levels were determined using label-free quantification based on peptide intensity with at least two pepti […]

library_books

First comprehensive analysis of lysine acetylation in Alvinocaris longirostris from the deep sea hydrothermal vents

2018
BMC Genomics
PMCID: 5946511
PMID: 29747590
DOI: 10.1186/s12864-018-4745-3

[…] The identified MS/MS data were analyzed by Maxquant search engine (v.1.5.2.8) [, ]. Tandem mass spectra were searched against a protein database of A. longirostris concatenated with reverse decoy database. The database was constructed with the […]

library_books

NS1 codon usage adaptation to humans in pandemic Zika virus

2018
PMCID: 5942634
PMID: 29768530
DOI: 10.1590/0074-02760170385

[…] ions. All identifications were filtered in order to achieve a FDR of less than 1%. Protein/peptide quantification was performed using the reporter ion MS2 module with the TMT 10-plex, embedded in the MaxQuant software. Protein quantification was performed using razor and unique peptides. Reporter ion intensities were given and assembled into the protein intensity. Each reporter ion intensity was c […]

call_split

Trafficking, localization and degradation of the Na+,HCO3− co transporter NBCn1 in kidney and breast epithelial cells

2018
Sci Rep
PMCID: 5943355
PMID: 29743600
DOI: 10.1038/s41598-018-25059-7
call_split See protocol

[…] ometry. Mass spectrometric analysis was performed by LC-MS using an Easy-LC system (Thermo) and an LTQOrbitrap or Q-Exactive mass spectrometer (Thermo Fisher). The raw data files were processed using MaxQuant (version 1.3.05). Data were blasted against Uniprot (http://www.uniprot.org/) human proteome dataset (release 2013_01, 87613 sequences) using the Andromeda search engine. […]

library_books

Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response

2018
PLoS Comput Biol
PMCID: 5940180
PMID: 29738528
DOI: 10.1371/journal.pcbi.1006088

[…] -band capping of missing channels), and the resultant intensity was not corrected for impurities or normalized for uneven mixing. The raw data corresponding to the Co-IP analyses were processed using MaxQuant (Version 1.5.2.8; []). Searches were performed against a target-decoy database of reviewed yeast proteins plus isoforms (Uniprot, downloaded January 20, 2013) using the Andromeda search algor […]

Citations

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MaxQuant institution(s)
Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany

MaxQuant review

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Marc Dubois's avatar image No country

Marc Dubois

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Desktop
Probably one of the best tools currently analyzing proteomic data: Andromeda, their search engine is very powerful, the algorithm for label-free quantification fast and reliable. The end of the pipeline is provided by Perseus, a statistical analysis tool.