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MaxQuant specifications


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


  • MaxLFQ


No version available


  • person_outline Juergen Cox

Publications for MaxQuant


MaxQuant goes Linux.

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

MaxQuant citations


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

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 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- […]


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

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 […]


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

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. [, ]. Tandem mass spectra were searched against a protein database of A. longirostris concatenated with reverse decoy database. The database was constructed with the […]


NS1 codon usage adaptation to humans in pandemic Zika virus

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 […]


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

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 ( human proteome dataset (release 2013_01, 87613 sequences) using the Andromeda search engine. […]


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

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; []). Searches were performed against a target-decoy database of reviewed yeast proteins plus isoforms (Uniprot, downloaded January 20, 2013) using the Andromeda search algor […]


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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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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.