The revolution and evolution of shotgun proteomics for large-scale proteome analysis.

Mass spectrometry has evolved at an exponential rate over the last 100 years. Innovations in the development of mass spectrometers have created powerful instruments capable of analyzing a wide range of targets, from rare atoms and molecules to very large molecules, such as a proteins, protein complexes, and DNA. These performance gains have been driven by sustaining innovations, punctuated by the occasional disruptive innovation. The use of mass spectrometry for proteome analysis was driven by disruptive innovations that created a capability for large-scale analysis of proteins and modifications.

[1]  Paul M Thomas,et al.  Evaluation of the compact high-field orbitrap for top-down proteomics of human cells. , 2012, Journal of proteome research.

[2]  S. Gygi,et al.  A high-throughput, multiplexed kinase assay using a benchtop orbitrap mass spectrometer to investigate the effect of kinase inhibitors on kinase signaling pathways. , 2012, Analytical chemistry.

[3]  S. Mohammed,et al.  In-house construction of a UHPLC system enabling the identification of over 4000 protein groups in a single analysis. , 2012, The Analyst.

[4]  Bryan P. Early,et al.  A Protease for Middle Down Proteomics , 2012, Nature Methods.

[5]  J. Kast,et al.  Advancing formaldehyde cross-linking towards quantitative proteomic applications , 2012, Analytical and Bioanalytical Chemistry.

[6]  John R Yates,et al.  Single-step inline hydroxyapatite enrichment facilitates identification and quantitation of phosphopeptides from mass-limited proteomes with MudPIT. , 2012, Journal of proteome research.

[7]  Daniel B. McClatchy,et al.  Dynamics of subcellular proteomes during brain development. , 2012, Journal of proteome research.

[8]  Albert J R Heck,et al.  Trends in ultrasensitive proteomics. , 2012, Current opinion in chemical biology.

[9]  Steven P Gygi,et al.  Hyperplexing: A Method for Higher-Order Multiplexed Quantitative Proteomics Provides a Map of the Dynamic Response to Rapamycin in Yeast , 2012, Science Signaling.

[10]  J. Yates,et al.  Extremely Long-Lived Nuclear Pore Proteins in the Rat Brain , 2012, Science.

[11]  A. Emili,et al.  Target Identification by Chromatographic Co-elution: Monitoring of Drug-Protein Interactions without Immobilization or Chemical Derivatization* , 2012, Molecular & Cellular Proteomics.

[12]  John R Yates,et al.  15N-labeled brain enables quantification of proteome and phosphoproteome in cultured primary neurons. , 2012, Journal of proteome research.

[13]  M. McKay,et al.  Multidimensional protein identification technology-selected reaction monitoring improving detection and quantification for protein biomarker studies. , 2012, Analytical chemistry.

[14]  Paul M Thomas,et al.  Robust analysis of the yeast proteome under 50 kDa by molecular-mass-based fractionation and top-down mass spectrometry. , 2012, Analytical chemistry.

[15]  Julian Mintseris,et al.  A Protein Complex Network of Drosophila melanogaster , 2011, Cell.

[16]  Jennifer M. Bolin,et al.  Proteomic and phosphoproteomic comparison of human ES and iPS cells , 2011, Nature Methods.

[17]  Richard D. LeDuc,et al.  Mapping Intact Protein Isoforms in Discovery Mode Using Top Down Proteomics , 2011, Nature.

[18]  J. Yates,et al.  Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT. , 2011, Journal of proteome research.

[19]  D. Chan,et al.  Analysis of the Human Endogenous Coregulator Complexome , 2011, Cell.

[20]  Daniel B. McClatchy,et al.  Differential Proteomic Analysis of Mammalian Tissues Using SILAM , 2011, PloS one.

[21]  Edward L. Huttlin,et al.  A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression , 2010, Cell.

[22]  J. Coon,et al.  Value of using multiple proteases for large-scale mass spectrometry-based proteomics. , 2010, Journal of proteome research.

[23]  S. Gygi,et al.  Sensitive multiplexed analysis of kinase activities and activity-based kinase identification , 2009, Nature Biotechnology.

[24]  J. Couzin-Frankel.  Genetics. The promise of a cure: 20 years and counting. , 2009, Science.

[25]  M. Mann,et al.  Universal sample preparation method for proteome analysis , 2009, Nature Methods.

[26]  J. Thomson,et al.  Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry , 2009, Proceedings of the National Academy of Sciences.

[27]  J. Yates,et al.  Multidimensional LC separations in shotgun proteomics. , 2008, Analytical chemistry.

[28]  M. Mann,et al.  SILAC Mouse for Quantitative Proteomics Uncovers Kindlin-3 as an Essential Factor for Red Blood Cell Function , 2008, Cell.

[29]  Christine C. Wu,et al.  A shotgun proteomic method for the identification of membrane-embedded proteins and peptides. , 2008, Journal of proteome research.

[30]  Daniel B. McClatchy,et al.  Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development. , 2007, Genome research.

[31]  Tao Xu,et al.  Quantitative Mass Spectrometry Identifies Insulin Signaling Targets in C. elegans , 2007, Science.

[32]  Guihua Yue,et al.  On-line 1D and 2D porous layer open tubular/LC-ESI-MS using 10-microm-i.d. poly(styrene-divinylbenzene) columns for ultrasensitive proteomic analysis. , 2007, Analytical chemistry.

[33]  John R Yates,et al.  15N metabolic labeling of mammalian tissue with slow protein turnover. , 2007, Journal of proteome research.

[34]  John R Yates,et al.  Relative quantification of stable isotope labeled peptides using a linear ion trap-Orbitrap hybrid mass spectrometer. , 2007, Analytical chemistry.

[35]  Jian Zhang,et al.  Ultratrace LC/MS proteomic analysis using 10-microm-i.d. Porous layer open tubular poly(styrene-divinylbenzene) capillary columns. , 2007, Analytical chemistry.

[36]  Steven P Gygi,et al.  A probability-based approach for high-throughput protein phosphorylation analysis and site localization , 2006, Nature Biotechnology.

[37]  John D. Venable,et al.  Automated ultra-high-pressure multidimensional protein identification technology (UHP-MudPIT) for improved peptide identification of proteomic samples. , 2006, Analytical chemistry.

[38]  Michelle S. Scott,et al.  Global Survey of Organ and Organelle Protein Expression in Mouse: Combined Proteomic and Transcriptomic Profiling , 2006, Cell.

[39]  Leigh Anderson,et al.  Quantitative Mass Spectrometric Multiple Reaction Monitoring Assays for Major Plasma Proteins* , 2006, Molecular & Cellular Proteomics.

[40]  M. Gorenstein,et al.  Simultaneous Qualitative and Quantitative Analysis of theEscherichia coli Proteome , 2006, Molecular & Cellular Proteomics.

[41]  P. Bork,et al.  Proteome survey reveals modularity of the yeast cell machinery , 2006, Nature.

[42]  Sean R. Collins,et al.  Global landscape of protein complexes in the yeast Saccharomyces cerevisiae , 2006, Nature.

[43]  M. Gorenstein,et al.  Absolute Quantification of Proteins by LCMSE , 2006, Molecular & Cellular Proteomics.

[44]  Dekel Tsur,et al.  Identification of post-translational modifications by blind search of mass spectra , 2005, Nature Biotechnology.

[45]  Michael K. Coleman,et al.  Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. , 2005, Analytical chemistry.

[46]  P. Roepstorff,et al.  Highly Selective Enrichment of Phosphorylated Peptides from Peptide Mixtures Using Titanium Dioxide Microcolumns* , 2005, Molecular & Cellular Proteomics.

[47]  Amy-Joan L Ham,et al.  Sample preparation and digestion for proteomic analyses using spin filters , 2005, Proteomics.

[48]  Tsuyoshi Tabata,et al.  Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards , 2005, Nature Biotechnology.

[49]  J. Yates,et al.  RNA-Dependent Cysteine Biosynthesis in Archaea , 2005, Science.

[50]  M. Washburn,et al.  The mammalian Mediator complex , 2005, FEBS letters.

[51]  K. Parker,et al.  Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*S , 2004, Molecular & Cellular Proteomics.

[52]  Yingyao Zhou,et al.  Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. , 2004, Genome research.

[53]  John D. Venable,et al.  Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra , 2004, Nature Methods.

[54]  Steven P Gygi,et al.  Large-scale characterization of HeLa cell nuclear phosphoproteins. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[55]  J. Yates,et al.  Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis. , 2004, Analytical chemistry.

[56]  J. Shabanowitz,et al.  Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[57]  Boris Zybailov,et al.  A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology. , 2004, Molecular cell.

[58]  J. Yates,et al.  A model for random sampling and estimation of relative protein abundance in shotgun proteomics. , 2004, Analytical chemistry.

[59]  Hiroshi Nakamura,et al.  Chemo-affinity of Titania for the Column-switching HPLC Analysis of Phosphopeptides , 2004, Analytical sciences : the international journal of the Japan Society for Analytical Chemistry.

[60]  Thomas P Conrads,et al.  A detergent‐ and cyanogen bromide‐free method for integral membrane proteomics: Application to Halobacterium purple membranes and the human epidermal membrane proteome , 2004, Proteomics.

[61]  J. Yates,et al.  A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. , 2003, Analytical chemistry.

[62]  M. Mann,et al.  Proteomic characterization of the human centrosome by protein correlation profiling , 2003, Nature.

[63]  Brian E Snydsman,et al.  Assigning function to yeast proteins by integration of technologies. , 2003, Molecular cell.

[64]  Marjan S. Bolouri,et al.  Integrated Analysis of Protein Composition, Tissue Diversity, and Gene Regulation in Mouse Mitochondria , 2003, Cell.

[65]  John R Yates,et al.  Nuclear Membrane Proteins with Potential Disease Links Found by Subtractive Proteomics , 2003, Science.

[66]  Jeroen Krijgsveld,et al.  Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics , 2003, Nature Biotechnology.

[67]  D. Goodlett,et al.  Shotgun collision‐induced dissociation of peptides using a time of flight mass analyzer , 2003, Proteomics.

[68]  J. Yates,et al.  A method for the comprehensive proteomic analysis of membrane proteins , 2003, Nature Biotechnology.

[69]  Andrew H. Thompson,et al.  Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. , 2003, Analytical chemistry.

[70]  S. Carr,et al.  N-Terminal peptide labeling strategy for incorporation of isotopic tags: a method for the determination of site-specific absolute phosphorylation stoichiometry. , 2002, Rapid communications in mass spectrometry : RCM.

[71]  Sheng Gu,et al.  Amino acid residue specific stable isotope labeling for quantitative proteomics. , 2002, Rapid communications in mass spectrometry : RCM.

[72]  Jonathan E. Allen,et al.  Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii , 2002, Nature.

[73]  David L. Tabb,et al.  A proteomic view of the Plasmodium falciparum life cycle , 2002, Nature.

[74]  Neil Hall,et al.  Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry , 2002, Nature.

[75]  Richard D. Smith,et al.  High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomics. , 2002, Analytical chemistry.

[76]  A. George.  Is the number of genes we possess limited by the presence of an adaptive immune system? , 2002, Trends in immunology.

[77]  John I. Clark,et al.  Shotgun identification of protein modifications from protein complexes and lens tissue , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[78]  M. Mann,et al.  Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics* , 2002, Molecular & Cellular Proteomics.

[79]  John R Yates,et al.  Multidimensional separations for protein/peptide analysis in the post-genomic era. , 2002, BioTechniques.

[80]  John R Yates,et al.  Analysis of quantitative proteomic data generated via multidimensional protein identification technology. , 2002, Analytical chemistry.

[81]  J. Shabanowitz,et al.  Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae , 2002, Nature Biotechnology.

[82]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[83]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[84]  C. Allis,et al.  Translating the Histone Code , 2001, Science.

[85]  T. Veenstra,et al.  Quantitative analysis of bacterial and mammalian proteomes using a combination of cysteine affinity tags and 15N-metabolic labeling. , 2001, Analytical chemistry.

[86]  J. Yates,et al.  Large-scale analysis of the yeast proteome by multidimensional protein identification technology , 2001, Nature Biotechnology.

[87]  M. Münchbach,et al.  Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentation-directing moiety. , 2000, Analytical chemistry.

[88]  Richard D. Smith,et al.  Accurate mass multiplexed tandem mass spectrometry for high-throughput polypeptide identification from mixtures. , 2000, Analytical chemistry.

[89]  J. Yates,et al.  Automated identification of amino acid sequence variations in proteins by HPLC/microspray tandem mass spectrometry. , 2000, Analytical chemistry.

[90]  B. Cravatt,et al.  Activity-based protein profiling: the serine hydrolases. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[91]  S. Gygi,et al.  Quantitative analysis of complex protein mixtures using isotope-coded affinity tags , 1999, Nature Biotechnology.

[92]  Nikola Tolić,et al.  High throughput proteome-wide precision measurements of protein expression using mass spectrometry , 1999 .

[93]  ロバート ジュニア フランザ，ビー,et al.  Stable isotope metabolic labeling for the analysis of biopolymers , 1999 .

[94]  J. Yates,et al.  Direct analysis of protein complexes using mass spectrometry , 1999, Nature Biotechnology.

[95]  F. Cross,et al.  Accurate quantitation of protein expression and site-specific phosphorylation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[96]  M. Gelb,et al.  Analysis of Rates of Multiple Enzymes in Cell Lysates by Electrospray Ionization Mass Spectrometry , 1999 .

[97]  John R Yates,et al.  The hMre11/hRad50 Protein Complex and Nijmegen Breakage Syndrome: Linkage of Double-Strand Break Repair to the Cellular DNA Damage Response , 1998, Cell.

[98]  D. Bier.  Stable isotopes in biosciences, their measurement and models for amino acid metabolism , 1997, European Journal of Pediatrics.

[99]  J. Jorgenson,et al.  Ultrahigh-pressure reversed-phase liquid chromatography in packed capillary columns. , 1997, Analytical chemistry.

[100]  J. Yates,et al.  Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low-femtomole level. , 1997, Analytical chemistry.

[101]  Terry D. Lee,et al.  A microscale electrospray interface for on-line, capillary liquid chromatography/tandem mass spectrometry of complex peptide mixtures. , 1995, Analytical chemistry.

[102]  J. Yates,et al.  Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. , 1995, Analytical chemistry.

[103]  J. Yates,et al.  Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. , 1995, Analytical chemistry.

[104]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[105]  R. Henderson,et al.  Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry. , 1992, Science.

[106]  C. G. Edmonds,et al.  New developments in biochemical mass spectrometry: electrospray ionization. , 1990, Analytical chemistry.

[107]  M. Mann,et al.  Electrospray ionization for mass spectrometry of large biomolecules. , 1989, Science.

[108]  J. Jorgenson,et al.  Preparation and evaluation of packed capillary liquid chromatography columns with inner diameters from 20 to 50 μm , 1989 .

[109]  B. Gibson,et al.  Analysis of the in vivo phosphorylation state of rabbit skeletal muscle glycogen synthase by fast-atom-bombardment mass spectrometry. , 1988, European journal of biochemistry.

[110]  Richard D. Smith,et al.  Capillary zone electrophoresis-MS , 1988, Nature.

[111]  H. Michel,et al.  Tandem mass spectrometry reveals that three photosystem II proteins of spinach chloroplasts contain N-acetyl-O-phosphothreonine at their NH2 termini. , 1988, The Journal of biological chemistry.

[112]  R. Caprioli,et al.  Continuous-flow sample probe for fast atom bombardment mass spectrometry. , 1986, Analytical chemistry.

[113]  J R Yates,et al.  Protein sequencing by tandem mass spectrometry. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[114]  J. Porath,et al.  Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography. , 1986, Analytical biochemistry.

[115]  G W Taylor,et al.  FAB-mapping of recombinant-DNA protein products. , 1983, Biochemical and biophysical research communications.

[116]  D. Hunt,et al.  Mixture analysis by triple-quadrupole mass spectrometry: metabolic profiling of urinary carboxylic acids. , 1982, Clinical chemistry.

[117]  S. Carr,et al.  Gas chromatographic mass spectrometric sequence determination of osteocalcin, a gamma-carboxyglutamic acid-containing protein from chicken bone. , 1981, The Journal of biological chemistry.

[118]  J. Shabanowitz,et al.  Sequence analysis of oligopeptides by secondary ion/collision activated dissociation mass spectrometry , 1981 .

[119]  M. Barber,et al.  Fast atom bombardment of solids as an ion source in mass spectrometry , 1981, Nature.

[120]  H. Morris,et al.  Fast atom bombardment: a new mass spectrometric method for peptide sequence analysis. , 1981, Biochemical and biophysical research communications.

[121]  W. Herlihy,et al.  Mass spectra of partial protein hydrolysates as a multiple phase check for long polypeptides deduced from DNA sequences: NH2-terminal segment of alanine tRNA synthetase. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[122]  A. Malcolm.  The decline and fall of protein chemistry? , 1978, Nature.

[123]  K. Biemann,et al.  Determination of the amino acid sequence of the C-terminal cyanogen bromide fragment of actin by computer-assisted gas chromatography--mass spectrometry. , 1973, Journal of the American Chemical Society.

[124]  M. Novotny,et al.  Capillary columns and their significance in biochemical research. , 1971, Chromatographic reviews.

[125]  G N Graham,et al.  Mass-spectrometric determination of the amino acid sequences in peptides isolated from the protein silk fibroin of Bombyx mori. , 1969, The Biochemical journal.

[126]  K. Biemann,et al.  Determination of the amino acid sequence in oligopeptides by computer interpretation of their high-resolution mass spectra. , 1966, Journal of the American Chemical Society.

[127]  K. Biemann,et al.  APPLICATION OF MASS SPECTROMETRY TO STRUCTURE PROBLEMS. I. AMINO ACID SEQUENCE IN PEPTIDES , 1959 .

[128]  R. Gohlke.  Time-of-Flight Mass Spectrometry and Gas-Liquid Partition Chromatography , 1959 .

[129]  A. Nier,et al.  Variations in the Relative Abundance of the Carbon Isotopes , 1939 .

[130]  F. W. A. M. D.Sc..  XLIV. The constitution of atmospheric neon , 1920 .

[131]  H. Gove,et al.  :Measuring Mass: From Positive Rays to Proteins , 2003 .

[132]  C. Enke,et al.  Practical implications of some recent studies in electrospray ionization fundamentals. , 2001, Mass spectrometry reviews.

[133]  J. Yates.  Mass spectrometry and the age of the proteome. , 1998, Journal of mass spectrometry : JMS.

[134]  John R. Yates,et al.  A STRATEGY FOR THE IDENTIFICATION OF PROTEINS LOCALIZED TO SUBCELLULAR SPACES : APPLICATION TO E. COLI PERIPLASMIC PROTEINS , 1997 .

[135]  Jimmy K. Eng,et al.  Tutorial review. Future prospects for the analysis of complex biological systems using micro-column liquid chromatography–electrospray tandem mass spectrometry , 1996 .

[136]  B. Gibson,et al.  Liquid secondary ion mass spectrometry of phosphorylated and sulfated peptides and proteins. , 1990, Methods in enzymology.

[137]  M. Goto,et al.  Direct coupling of micro high-performance liquid chromatography with fast atom bombardment mass spectrometry. II. Application to gradient elution of bile acids. , 1986, Journal of chromatography.

[138]  B. Gibson,et al.  A mass spectrometric method for the identification of novel peptides in Xenopus laevis skin secretions. , 1986, Journal of natural products.

[139]  H. Khorana,et al.  Partial primary structure of bacteriorhodopsin: sequencing methods for membrane proteins. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[140]  K. Biemann,et al.  On the structure of lysopine, a new amino acid isolated from crown gall tissue. , 1960, Biochimica et biophysica acta.

[141]  Methods : A Companion to Methods in Enzymology , 2022 .