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MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
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 describe… Expand
Andromeda: a peptide search engine integrated into the MaxQuant environment.
- J. Cox, Nadin Neuhauser, Annette Michalski, R. Scheltema, J. V. Olsen, M. Mann
- Chemistry, Medicine
- Journal of proteome research
- 22 February 2011
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 engine… Expand
The Perseus computational platform for comprehensive analysis of (prote)omics data
- S. Tyanova, Tikira Temu, +5 authors J. Cox
- Biology, Medicine
- Nature Methods
- 1 September 2016
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 the… Expand
Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ *
- J. Cox, M. Y. Hein, Christian A. Luber, Igor Paron, N. Nagaraj, M. Mann
- Biology, Medicine
- Molecular & Cellular Proteomics
- 17 June 2014
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 remains… Expand
The MaxQuant computational platform for mass spectrometry-based shotgun proteomics
- S. Tyanova, Tikira Temu, J. Cox
- Biology, Medicine
- Nature Protocols
- 1 December 2016
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 can… Expand
The PRIDE database and related tools and resources in 2019: improving support for quantification data
- Yasset Pérez-Riverol, A. Csordas, +20 authors J. Vizcaíno
- Biology, Computer Science
- Nucleic Acids Res.
- 5 November 2018
TLDR
A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics
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Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis
- J. V. Olsen, M. Vermeulen, +9 authors M. Mann
- Biology, Medicine
- Science Signaling
- 12 January 2010
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 cellular… Expand
A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances
- M. Y. Hein, Nina C. Hubner, +9 authors M. Mann
- Biology, Medicine
- Cell
- 22 October 2015
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 connected… Expand
1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data
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