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

Abstract

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 MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data. Using correlation analysis and graph theory, MaxQuant 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. By integrating multiple mass measurements and correcting for linear and nonlinear mass offsets, we achieve mass accuracy in the p.p.b. range, a sixfold increase over standard techniques. We increase the proportion of identified fragmentation spectra to 73% for SILAC peptide pairs via unambiguous assignment of isotope and missed-cleavage state and individual mass precision. MaxQuant automatically quantifies several hundred thousand peptides per SILAC-proteome experiment and allows statistically robust identification and quantification of >4,000 proteins in mammalian cell lysates.

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Figure 1: Three-dimensional peak detection.
Figure 2: Automatic large-scale SILAC pair detection.
Figure 3: Accurate masses and individual peptide mass errors.
Figure 4: Peptide score (P-score) distributions.
Figure 5: High rate of identified MS/MS spectra.
Figure 6: Proteome-wide accurate quantification and significance.

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Acknowledgements

We thank all the other members of the Proteomics and Signal Transduction group for help with the development of MaxQuant. Shubin Ren helped in developing the 3D data viewer used in MaxQuant. Nina Hubner measured the data used in this analysis. This work was supported by the Max-Planck Society and by the 6th Framework Program of the European Union (Interaction Proteome LSHG-CT-2003-505520 and HEROIC LSHG-CT-2005-018883).

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Correspondence to Jürgen Cox or Matthias Mann.

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Cox, J., Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26, 1367–1372 (2008). https://doi.org/10.1038/nbt.1511

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