• Publications
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MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
  • J. Cox, M. Mann
  • Chemistry, Medicine
  • Nature Biotechnology
  • 30 November 2008
Efficient analysis of very large amounts of raw data for peptide identification and protein quantification is a principal challenge in mass spectrometry (MS)-based proteomics. Here we describeExpand
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Andromeda: a peptide search engine integrated into the MaxQuant environment.
A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel peptide search engineExpand
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The Perseus computational platform for comprehensive analysis of (prote)omics data
A main bottleneck in proteomics is the downstream biological analysis of highly multivariate quantitative protein abundance data generated using mass-spectrometry-based analysis. We developed theExpand
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Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ *
Protein quantification without isotopic labels has been a long-standing interest in the proteomics field. However, accurate and robust proteome-wide quantification with label-free approaches remainsExpand
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The MaxQuant computational platform for mass spectrometry-based shotgun proteomics
MaxQuant is one of the most frequently used platforms for mass-spectrometry (MS)-based proteomics data analysis. Since its first release in 2008, it has grown substantially in functionality and canExpand
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The PRIDE database and related tools and resources in 2019: improving support for quantification data
We summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in 2016. Expand
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A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics
MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. Expand
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Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis
Protein phosphorylation during the cell cycle may be an all-or-none process in many instances. All-or-None Phosphorylation Phosphorylation is a key regulatory event that drives many cellularExpand
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A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances
The organization of a cell emerges from the interactions in protein networks. The interactome is critically dependent on the strengths of interactions and the cellular abundances of the connectedExpand
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1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data
  • J. Cox, M. Mann
  • Biology, Medicine
  • BMC Bioinformatics
  • 5 November 2012
We describe a new method, 2D annotation enrichment, which compares quantitative data from any two 'omics' types in the context of categorical annotation of the proteins or genes. Expand
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