Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

Aebersold, 2003, Mass spectrometry-based proteomics, Nature, 422, 198, 10.1038/nature01511

Ong, 2005, Mass spectrometry-based proteomics turns quantitative, Nat. Chem. Biol, 1, 252, 10.1038/nchembio736

Bantscheff, 2007, Quantitative mass spectrometry in proteomics: a critical review, Anal. Bioanal. Chem, 389, 1017, 10.1007/s00216-007-1486-6

Cox, 2007, Is proteomics the new genomics?, Cell, 130, 395, 10.1016/j.cell.2007.07.032

Altelaar, 2013, Next-generation proteomics: towards an integrative view of proteome dynamics, Nat. Rev. Genet, 14, 35, 10.1038/nrg3356

Mann, 2013, The coming age of complete, accurate, and ubiquitous proteomes, Mol. Cell, 49, 583, 10.1016/j.molcel.2013.01.029

Dephoure, 2012, Hyperplexing: a method for higher-order multiplexed quantitative proteomics provides a map of the dynamic response to rapamycin in yeast, Sci. Signal, 5, rs2, 10.1126/scisignal.2002548

Listgarten, 2005, Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry, Mol. Cell. Proteomics, 4, 419, 10.1074/mcp.R500005-MCP200

Domon, 2006, Mass spectrometry and protein analysis, Science, 312, 212, 10.1126/science.1124619

Mueller, 2008, An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data, J. Proteome Res, 7, 51, 10.1021/pr700758r

Nahnsen, 2012, Tools for label-free peptide quantification, Mol. Cell. Proteomics, 12, 549, 10.1074/mcp.R112.025163

Bantscheff, 2012, Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present, Anal. Bioanal. Chem, 404, 939, 10.1007/s00216-012-6203-4

Matzke, 2013, A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments, Proteomics, 13, 493, 10.1002/pmic.201200269

Mueller, 2007, SuperHirn—a novel tool for high resolution LC-MS-based peptide/protein profiling, Proteomics, 7, 3470, 10.1002/pmic.200700057

Bellew, 2006, A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS, Bioinformatics, 22, 1902, 10.1093/bioinformatics/btl276

Rauch, 2006, Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments, J. Proteome Res, 5, 112, 10.1021/pr0503533

May, 2007, A platform for accurate mass and time analyses of mass spectrometry data, J. Proteome Res, 6, 2685, 10.1021/pr070146y

Jaffe, 2006, PEPPeR, a platform for experimental proteomic pattern recognition, Mol. Cell. Proteomics, 5, 1927, 10.1074/mcp.M600222-MCP200

Kohlbacher, 2007, TOPP—the OpenMS proteomics pipeline, Bioinformatics, 23, e191, 10.1093/bioinformatics/btl299

Palagi, 2005, MSight: an image analysis software for liquid chromatography-mass spectrometry, Proteomics, 5, 2381, 10.1002/pmic.200401244

Johansson, 2006, Differential expression analysis of Escherichia coli proteins using a novel software for relative quantitation of LC-MS/MS data, Proteomics, 6, 4475, 10.1002/pmic.200500921

Roy, 2007, Quantification of proteins and metabolites by mass spectrometry without isotopic labeling, Methods Mol. Biol, 359, 87, 10.1007/978-1-59745-255-7_6

Katajamaa, 2006, MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data, Bioinformatics, 22, 634, 10.1093/bioinformatics/btk039

Leptos, 2006, MapQuant: open-source software for large-scale protein quantification, Proteomics, 6, 1770, 10.1002/pmic.200500201

Smith, 2002, An accurate mass tag strategy for quantitative and high-throughput proteome measurements, Proteomics, 2, 513, 10.1002/1615-9861(200205)2:5<513::AID-PROT513>3.0.CO;2-W

Old, 2005, Comparison of label-free methods for quantifying human proteins by shotgun proteomics, Mol. Cell. Proteomics, 4, 1487, 10.1074/mcp.M500084-MCP200

Sturm, 2008, OpenMS—an open-source software framework for mass spectrometry, BMC Bioinformatics, 9, 163, 10.1186/1471-2105-9-163

Listgarten, 2007, Difference detection in LC-MS data for protein biomarker discovery, Bioinformatics, 23, e198, 10.1093/bioinformatics/btl326

Park, 2008, A quantitative analysis software tool for mass spectrometry-based proteomics, Nat. Methods, 5, 319, 10.1038/nmeth.1195

Bridges, 2007, ProtQuant: a tool for the label-free quantification of MudPIT proteomics data, BMC Bioinformatics, 8, S24, 10.1186/1471-2105-8-S7-S24

Weisser, 2013, An automated pipeline for high-throughput label-free quantitative proteomics, J. Proteome Res, 10.1021/pr300992u

Ning, 2012, Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data, J. Proteome Res, 11, 2261, 10.1021/pr201052x

Cheng, 2009, Absolute protein quantification by LC/MS(E) for global analysis of salicylic acid-induced plant protein secretion responses, J. Proteome Res, 8, 82, 10.1021/pr800649s

Polpitiya, 2008, DAnTE: a statistical tool for quantitative analysis of -omics data, Bioinformatics, 24, 1556, 10.1093/bioinformatics/btn217

Karpievitch, 2009, A statistical framework for protein quantitation in bottom-up MS-based proteomics, Bioinformatics, 25, 2028, 10.1093/bioinformatics/btp362

Clough, 2009, Protein quantification in label-free LC-MS experiments, J. Proteome Res, 8, 5275, 10.1021/pr900610q

Choi, 2012, SAINT-MS1: protein-protein interaction scoring using label-free intensity data in affinity purification-mass spectrometry experiments, J. Proteome Res, 11, 2619, 10.1021/pr201185r

Ong, 2002, Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics, Mol. Cell. Proteomics, 1, 376, 10.1074/mcp.M200025-MCP200

Gygi, 1999, Quantitative analysis of complex protein mixtures using isotope-coded affinity tags, Nat. Biotechnol, 17, 994, 10.1038/13690

Ross, 2004, Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents, Mol. Cell. Proteomics, 3, 1154, 10.1074/mcp.M400129-MCP200

Boersema, 2008, Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates, Proteomics, 8, 4624, 10.1002/pmic.200800297

Cox, 2008, MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification, Nat. Biotechnol, 26, 1367, 10.1038/nbt.1511

Andersen, 2003, Proteomic characterization of the human centrosome by protein correlation profiling, Nature, 426, 570, 10.1038/nature02166

Ishihama, 2005, Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein, Mol. Cell. Proteomics, 4, 1265, 10.1074/mcp.M500061-MCP200

Hubner, 2008, Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis, Proteomics, 4862, 10.1002/pmic.200800351

Rappsilber, 2003, Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics, Anal. Chem, 75, 663, 10.1021/ac026117i

Olsen, 2005, Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap, Mol. Cell. Proteomics, 4, 2010, 10.1074/mcp.T500030-MCP200

Cox, 2008, How much peptide sequence information is contained in ion trap tandem mass spectra?, J. Am. Soc. Mass Spectrom, 19, 1813, 10.1016/j.jasms.2008.07.024

Geiger, 2012, Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins, Mol. Cell. Proteomics, 11, 10.1074/mcp.M111.014050

Cox, 2011, Andromeda: a peptide search engine integrated into the MaxQuant environment, J. Proteome Res, 10, 1794, 10.1021/pr101065j

Press, 2007

de Godoy, 2008, Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast, Nature, 455, 1251, 10.1038/nature07341

Schwanhausser, 2011, Global quantification of mammalian gene expression control, Nature, 473, 337, 10.1038/nature10098

Wisniewski, 2012, Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma, Mol. Syst. Biol, 8, 611, 10.1038/msb.2012.44

Tusher, 2001, Significance analysis of microarrays applied to the ionizing radiation response, Proc. Natl. Acad. Sci. U.S.A, 98, 5116, 10.1073/pnas.091062498

Hubner, 2010, Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions, J. Cell Biol, 189, 739, 10.1083/jcb.200911091

Eberl, 2013, A map of general and specialized chromatin readers in mouse tissues generated by label-free interaction proteomics, Mol. Cell, 49, 368, 10.1016/j.molcel.2012.10.026

Luber, 2010, Quantitative proteomics reveals subset-specific viral recognition in dendritic cells, Immunity, 32, 279, 10.1016/j.immuni.2010.01.013

Meissner, 2013, Direct proteomic quantification of the secretome of activated immune cells, Science, 340, 475, 10.1126/science.1232578

Batruch, 2012, Analysis of seminal plasma from patients with non-obstructive azoospermia and identification of candidate biomarkers of male infertility, J. Proteome Res, 11, 1503, 10.1021/pr200812p

Boerries, 2013, Molecular fingerprinting of the podocyte reveals novel gene and protein regulatory networks, Kidney Int, 83, 1052, 10.1038/ki.2012.487

de Godoy, 2012, Quantitative proteomics of Trypanosoma cruzi during metacyclogenesis, Proteomics, 12, 2694, 10.1002/pmic.201200078

Lopez-Contreras, 2013, A proteomic characterization of factors enriched at nascent DNA molecules, Cell Rep, 3, 1105, 10.1016/j.celrep.2013.03.009

Smaczniak, 2012, Proteomics-based identification of low-abundance signaling and regulatory protein complexes in native plant tissues, Nat. Protoc, 7, 2144, 10.1038/nprot.2012.129

Gamez-Pozo, 2013, Shotgun proteomics of archival triple-negative breast cancer samples, Proteomics Clin. Appl, 7, 283, 10.1002/prca.201200048

Sakurai, 2013, Identification of a metabolizing enzyme in human kidney by proteomic correlation profiling, Mol. Cell. Proteomics, 12, 2313, 10.1074/mcp.M112.023853

Liu, 2012, Proteomics pipeline for biomarker discovery of laser capture microdissected breast cancer tissue, J. Mammary Gland Biol. Neoplasia, 17, 155, 10.1007/s10911-012-9252-6

Tao, 2013, Quantitative proteomic analysis reveals the neuroprotective effects of huperzine A for amyloid beta treated neuroblastoma N2a cells, Proteomics, 13, 1314, 10.1002/pmic.201200437

Craven, 2013, Proteomic analysis of formalin-fixed paraffin-embedded renal tissue samples by label-free MS: assessment of overall technical variability and the impact of block age, Proteomics Clin. Appl, 7, 273, 10.1002/prca.201200065

Hogl, 2013, Label-free quantitative analysis of the membrane proteome of Bace1 protease knock-out zebrafish brains, Proteomics, 13, 1519, 10.1002/pmic.201200582

Tsai, 2012, Label-free quantitative proteomics of CD133-positive liver cancer stem cells, Proteome Sci, 10, 69, 10.1186/1477-5956-10-69

Aye, 2012, Reorganized PKA-AKAP associations in the failing human heart, J. Mol. Cell. Cardiol, 52, 511, 10.1016/j.yjmcc.2011.06.003

Merl, 2012, Direct comparison of MS-based label-free and SILAC quantitative proteome profiling strategies in primary retinal Muller cells, Proteomics, 12, 1902, 10.1002/pmic.201100549

Sessler, 2012, Analysis of the Plasmodium falciparum proteasome using Blue Native PAGE and label-free quantitative mass spectrometry, Amino Acids, 43, 1119, 10.1007/s00726-012-1296-9

Zelenak, 2011, Proteome analysis of erythrocytes lacking AMP-activated protein kinase reveals a role of PAK2 kinase in eryptosis, J. Proteome Res, 10, 1690, 10.1021/pr101004j

Michalski, 2012, Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes, Mol. Cell. Proteomics, 11, 10.1074/mcp.O111.013698

Michalski, 2011, Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer, Mol. Cell. Proteomics, 10, 10.1074/mcp.M111.011015