MaxQuant protocols

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MaxQuant computational protocol

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


Add your version

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 IN pipelines

 (37)
2018
PMCID: 5772234
PMID: 29150517
DOI: 10.1128/AEM.02091-17

[…] recorded with xcalibur software 2.2 sp1.48 (thermo scientific)., proteins under both culture conditions were identified with andromeda (82) and quantified with the lfq algorithm (25) embedded in maxquant version 1.5.3.175 (81). the fasta protein database for identification was taken from the output of the functional annotation of the chromosome and contained 2,486 entries. […]

2018
PMCID: 5778013
PMID: 29358734
DOI: 10.1038/s41467-017-02694-8

[…] (v.1.4.0.8). 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 1.5.3.1256. for protein identification, spectra were correlated with the s. cerevisiae protein database (uniprotkb canonical set including isoforms for strain ac204508/s288c, proteome id […]

2018
PMCID: 5788924
PMID: 29379051
DOI: 10.1038/s41598-018-20130-9

[…] areas were calculated using the precursor ions area detector node., identification and label-free quantification of ubiquitinated peptides in hela cells was performed using the andromeda56 and the maxlfq algorithm57, respectively, implemented in the maxquant computational proteomics platform (v1.5.1.2)58. ms2 spectra were searched against the human uniprot complete proteome set including […]

2018
PMCID: 5788924
PMID: 29379051
DOI: 10.1038/s41598-018-20130-9

[…] detector node., identification and label-free quantification of ubiquitinated peptides in hela cells was performed using the andromeda56 and the maxlfq algorithm57, respectively, implemented in the maxquant computational proteomics platform (v1.5.1.2)58. ms2 spectra were searched against the human uniprot complete proteome set including isoforms, the cpxv br database and a contaminant database […]

2018
PMCID: 5836539
PMID: 29507054
DOI: 10.15252/msb.20177858

[…] with 0.6% acetic acid. the samples were loaded and washed with 0.6% acetic acid and eluted with 80% acn/0.6% acetic acid., label‐free quantification was performed by analyzing the raw data by maxquant (version 1.5.3.30; cox & mann, 2008). andromeda (cox et al, 2011) was used to search the ms/ms data against the uniprot homo sapiens database (containing canonical and isoforms_42144 […]

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

MaxQuant review

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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.