MaxQuant statistics

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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


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  • person_outline Juergen Cox <>

Publications for MaxQuant


MaxQuant goes Linux.

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

MaxQuant in pipelines

PMCID: 5772234
PMID: 29150517
DOI: 10.1128/AEM.02091-17

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

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

[…] (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: 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 andromeda and the maxlfq algorithm, respectively, implemented in the maxquant computational proteomics platform (v1.5.1.2). ms2 spectra were searched against the human uniprot complete proteome set including isoforms, […]

PMCID: 5805371
PMID: 29377895
DOI: 10.1371/journal.pgen.1007189

[…] maximum injection time 120 ms, isolation window 1.4 m/z, nce 27%, and underfill ratio of 20%), and finally detected in the orbitrap (r = 15,000 at 200 m/z)., the raw ms files were processed using maxquant (version with the integrated andromeda search engine using fdr < 0.01 []. variable modifications for oxidized methionine (m) and acetylation (protein n-term) as well as a fixed […]

PMCID: 5830946
PMID: 29358085
DOI: 10.1016/j.stemcr.2017.12.016

[…] supplemented with mgcl2 to 1.5 mm and incubated at 4°c for 2 hr before proceeding with immunoprecipitation as above., thermo raw files from tandem mass spectrometry (ms/ms) were analyzed using maxquant (, ) version and searched against the reviewed mus musculus swiss-prot proteome database using the following parameters: trypsin/p digest enzyme with strict trypsin specificity; […]

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MaxQuant in publications

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

[…] 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- […]

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

[…] 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 […]

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

[…] automatic gain control (agc) was performed to prevent overfilling of the orbitrap and 5e4 ions were accumulated for generation of ms/ms spectra., 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 […]

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

[…] was set to 1e5 with a maximum injection time of 150 ms and isolation window of 1.2 m/z. the raw files are available from the authors upon request., database search - raw data were searched with maxquant () and the database search engine andromeda. uniprot database contained human proteins, zika virus proteins (pe_243 and mr_766) and common contaminants. ms accuracy was set to 4.5 ppm […]

PMCID: 5943355
PMID: 29743600
DOI: 10.1038/s41598-018-25059-7

[…] 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., proximity […]

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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.