MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

By Jüergen Cox, Matthias Mann. Nature Biotechnology, 2008

14,691 citations recorded by the source corpus.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/a968620dcf399d7d7f89f98dc1d3da8c114dac8d

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Citations in the corpus

TopBP1 utilises a bipartite GINS binding mode to activate the 1 replicative helicase 2 (methodology): “0.3.0) using the default settings (Cox & Mann 2008) 76.”
The Failing Heart Relies on Ketone Bodies as a Fuel (2016, background): “38 Ech1 Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase -1.”
Triacylglycerol synthesis enzymes mediate lipid droplet growth by relocalizing from the ER to lipid droplets. (2013, positive): “19 (http://maxquant.org/downloads.htm; Cox and Mann, 2008).”
jPOSTrepo: an international standard data repository for proteomes (2016, methodology): “mzIdentML (19) and mzTab (20); commonly used software, such as Mascot (21), X!Tandem (22) and MaxQuant (23) and the settings used in database searches.”
Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics (2015, background): “Although there are a tremendous number of individual tools for processing proteomics data [6] and some developed as pipelines [7,8], the Trans-Proteomic Pipeline (TPP; [9,10]) is the most widely used free and open-source complete suite of tools for processing shotgun proteomics data with statistical”
Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology (2015, neutral): “5 (25) using default parameters except the setting for “Top MS/MS peaks per 100 Da” being set to 100.”
Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy (2018, methodology): “Raw files were processed with MaxQuant (v. 1.5.2.8) 27 to generate peak files (APL format), with “ Top MS/MS peaks per 100 Da ” set to 100.”
The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update (2024, positive): “In some cases, development of an open-source equivalent has minimal delay after commercial solutions become available; MaxQuant ( 11 ) as a pan-proteomics tool is one such example.”
An insight into iTRAQ: where do we stand now? (2012, background): “Modelling is opening up perspectives for proteomics, paving the way to better understand the iTRAQ or instrument bias [29] and how to more effectively use the available data [62].”
Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ (2014, methodology): “Software and Data Availability—The label-free software MaxLFQ is completely integrated into the MaxQuant software (42) and can be activated by one additional click.”