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


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MaxQuant articles


MaxQuant goes Linux.

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

MaxQuant citations

PMCID: 5863380

[…] and the following variable modifications; deamidation (n), deamidation (q) and oxidation (m). fragment mass tolerance was set to ± 0.05 da., further analysis of ms raw data was performed using the maxquant (v1.6.0.1) [24] and perseus (v1.6.0.2) [25] programs. proteins were identified by searching raw data against the uniprot reference human proteome database (may 2017 version, 93591 sequences) […]

PMCID: 5778013

[…] (v. artificial within groups’ variance was set to zero and the p-value was used for truncation with a threshold of 0.05., ms raw data of dimethyl-labelled samples were jointly processed by maxquant for protein identification, spectra were correlated with the s. cerevisiae protein database (uniprotkb canonical set including isoforms for strain ac204508/s288c, proteome id […]

PMCID: 5620370

[…] event. full-scan data were acquired in profile, and fragments were analyzed in centroid mode by xcalibur software. the lc unit was controlled by chromeleon xpress software., for data analysis, maxquant (cox and mann, 2008), perseus (tyanova et al., 2016), and excel (microsoft office 2013) were used. the enzyme specificity was set to trypsin, and missed cleavages […]

PMCID: 4792069

[…] with which the data were searched against a uniprot human database with a list of common contaminants appended, to ascertain the protein identifications of the gel bands, the data were searched with maxquant (v1.2.2.5) against a database containing the sequences of the identified proteins. the data were searched with the following modifications: carbamidomethyl (c; fixed) and phospho (sty) […]

PMCID: 4633731

[…] and carbamidomethylation was set as a fixed modification. label-free protein quantification was performed using a previously described label-free quantification (lfq) algorithm implemented in the maxquant software with a 2 min window for matching between runs and maximum 1% peptide and 1% protein fdr5152. protein intensity values were normalized using the lfq algorithm available […]

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.