MaxQuant publications

The MaxQuant paper. Note that it has a large supplement containing in-depth descriptions of algorithms.

Cox, J. and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26, 1367-72.

The first major application of MaxQuant in proteome-wide SILAC-based quantification.

de Godoy LM, Olsen JV, Cox J, Nielsen ML, Hubner NC, Fröhlich F, Walther TC, Mann M. (2008) Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455, 1251-4.

Andromeda search engine.

Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M. (2011) Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res 10, 1794-805.

A paper describing algorithmic developments for mass accuracy improvements.

Cox, J. and Mann, M. (2009) Computational principles of determining and improving mass precision and accuracy for proteome measurements in an Orbitrap. J Am Soc Mass Spectrom 20, 1477-85.

A protocol applicable to 1.0.X.Y versions.

Cox J, Matic I, Hilger M, Nagaraj N, Selbach M, Olsen JV, Mann M. . (2009) A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat Protoc 4, 698-705.

First application of the label free quantification algorithm.

Luber CA, Cox J, Lauterbach H, Fancke B, Selbach M, Tschopp J, Akira S, Wiegand M, Hochrein H, O'Keeffe M, Mann M. (2010) Quantitative proteomics reveals subset-specific viral recognition in dendritic cells. Immunity 32, 279-89.

Large-scale phosphoproteomics application including calculation of site occupancies.

Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M. (2010) Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal 3, ra3.

All ion fragmentation.

Geiger T, Cox J, Mann M. (2010) Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation. Mol Cell Proteomics 9, 2252-61.

Software lock mass. Joint recalibration of time and mass dependent mass errors.

Cox, J., Michalski, A. and Mann, M. (2011) Software lock mass by two dimensional minimization of peptide mass errors. J Am Soc Mass Spectrom 22, 1373-80.

Coming soon

Matching between runs.

Related reviews

Cox, J. and Mann, M. (2011) Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology. Annu Rev Biochem .

Cox, J. and Mann, M. (2007) Is proteomics the new genomics? Cell 130, 395-8.

Selected applications

Lundberg E, Fagerberg L, Klevebring D, Matic I, Geiger T, Cox J, Algenäs C, Lundeberg J, Mann M, Uhlen M. (2010) Defining the transcriptome and proteome in three functionally different human cell lines. Mol Syst biol 6, 450.

Geiger T, Cox J, Mann M. (2010) Proteomic changes resulting from gene copy number variations in cancer cells. PLoS Genet 6, e1001090.

Michalski A, Cox J, Mann M. (2011) More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J Proteome Res 10, 1785-93.

Geiger T, Cox J, Ostasiewicz P, Wisniewski JR, Mann M. (2010) Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat Methods 7, 383-5.

Michalski A, Damoc E, Hauschild JP, Lange O, Wieghaus A, Makarov A, Nagaraj N, Cox J, Mann M, Horning S. (2011) Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol Cell Proteomics.

Sharma K, Weber C, Bairlein M, Greff Z, Keri G, Cox J, Olsen J, Daub H. (2009) Proteomics strategy for quantitative protein interaction profiling in cell extracts. Nat Methods 6, 741-4.

Geiger T, Wisniewski JR, Cox J, Zanivan S, Kruger M, Ishihama Y, Mann M. (2011) Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics. Nat Protoc 6, 147-57.

Thakur SS, Geiger T, Chatterjee B, Bandilla P, Froehlich F, Cox J, Mann M. (2011) Deep and highly sensitive proteome coverage by LC-MS/MS without pre-fractionation. Mol Cell Proteomics.

Hubner NC, Bird AW, Cox J, Splettstoesser B, Bandilla P, Poser I, Hyman A, Mann M. (2010) Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. Journal of Cell Biology 189, 739-754.

Ohta S, Bukowski-Wills JC, Sanchez-Pulido L, Alves Fde L, Wood L, Chen ZA, Platani M, Fischer L, Hudson DF, Ponting CP, Fukagawa T, Earnshaw WC, Rappsilber J. (2010) The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics. Cell 142, 810-21.

Schwanhäusser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M. (2011) Global quantification of mammalian gene expression control. Nature 473, 337-42.