• Publications
  • Influence
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
MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data, detects peaks, isotope clusters and stable amino acid isotope–labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space and achieves mass accuracy in the p.p.b. range. Expand
Andromeda: a peptide search engine integrated into the MaxQuant environment.
A novel peptide search engine using a probabilistic scoring model that can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, and accommodates extremely large databases. Expand
Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics*
SILAC is a simple, inexpensive, and accurate procedure that can be used as a quantitative proteomic approach in any cell culture system and is applied to the relative quantitation of changes in protein expression during the process of muscle cell differentiation. Expand
The Perseus computational platform for comprehensive analysis of (prote)omics data
The Perseus software platform was developed to support biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data and it is anticipated that Perseus's arsenal of algorithms and its intuitive usability will empower interdisciplinary analysis of complex large data sets. Expand
Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ *
A new intensity determination and normalization procedure called MaxLFQ is developed that is fully compatible with any peptide or protein separation prior to LC-MS analysis, which accurately detects the mixing ratio over the entire protein expression range, with greater precision for abundant proteins. Expand
Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips
StageTips are ordinary pipette tips containing very small disks made of beads with reversed phase, cation-exchange or anion-ex exchange surfaces embedded in a Teflon mesh that allow flexible combination of disks with different surfaces to obtain multi-functional tips. Expand
Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions
A proteomic-scale analysis of protein acetylation suggests that it is an important biological regulatory mechanism and the regulatory scope of lysine acetylations is broad and comparable with that of other major posttranslational modifications. Expand
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
Comparison of the HMS-PCI data set with interactions reported in the literature revealed an average threefold higher success rate in detection of known complexes compared with large-scale two-hybrid studies. Expand
Mass spectrometry-based proteomics
The ability of mass spectrometry to identify and, increasingly, to precisely quantify thousands of proteins from complex samples can be expected to impact broadly on biology and medicine. Expand
In-gel digestion for mass spectrometric characterization of proteins and proteomes
This protocol is for the in-gel digestion of both silver and Coomassie-stained protein spots or bands and can be followed by MALDI-MS or LC-MS/MS analysis to identify proteins at sensitivities better than a few femtomoles of protein starting material. Expand