Quantitative proteomics in biological research

Proteomics has enabled the direct investigation of biological material, at first through the analysis of individual proteins, then of lysates from cell cultures, and finally of extracts from tissues and biopsies from entire organisms. Its latest manifestation – quantitative proteomics – allows deeper insight into biological systems. This article reviews the different methods used to extract quantitative information from mass spectra. It follows the technical developments aimed toward global proteomics, the attempt to characterize every expressed protein in a cell by at least one peptide. When applications of the technology are discussed, the focus is placed on yeast biology. In particular, differential quantitative proteomics, the comparison between an experiment and its control, is very discriminating for proteins involved in the process being studied. When trying to understand biological processes on a molecular level, differential quantitative proteomics tends to give a clearer picture than global transcription analyses. As a result, MS has become an even more indispensable tool for biochemically motivated biological research.

[1]  P. Greengard,et al.  Writing Memories with Light-Addressable Reinforcement Circuitry , 2009, Cell.

[2]  Nicholas T. Ingolia,et al.  Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling , 2009, Science.

[3]  A. Chakraborty,et al.  Comparison of 1‐D and 2‐D LC MS/MS methods for proteomic analysis of human serum , 2009, Electrophoresis.

[4]  M. Mann,et al.  Comparative Proteomic Phenotyping of Cell Lines and Primary Cells to Assess Preservation of Cell Type-specific Functions , 2009, Molecular & Cellular Proteomics.

[5]  R. Aebersold,et al.  Evolution of organelle-associated protein profiling. , 2009, Journal of proteomics.

[6]  Reinout Raijmakers,et al.  Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics , 2009, Nature Protocols.

[7]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[8]  P. Greengard,et al.  A Translational Profiling Approach for the Molecular Characterization of CNS Cell Types , 2008, Cell.

[9]  Henry H. N. Lam,et al.  A database of mass spectrometric assays for the yeast proteome , 2008, Nature Methods.

[10]  M. Mann,et al.  Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast , 2008, Nature.

[11]  R. Aebersold,et al.  Selected reaction monitoring for quantitative proteomics: a tutorial , 2008, Molecular systems biology.

[12]  N. Rajewsky,et al.  Widespread changes in protein synthesis induced by microRNAs , 2008, Nature.

[13]  D. Bartel,et al.  The impact of microRNAs on protein output , 2008, Nature.

[14]  Bernhard Kuster,et al.  Robust and Sensitive iTRAQ Quantification on an LTQ Orbitrap Mass Spectrometer*S , 2008, Molecular & Cellular Proteomics.

[15]  L. F. Waanders,et al.  A Novel Chromatographic Method Allows On-line Reanalysis of the Proteome*S⃞ , 2008, Molecular & Cellular Proteomics.

[16]  Nichole L. King,et al.  Targeted Quantitative Analysis of Streptococcus pyogenes Virulence Factors by Multiple Reaction Monitoring*S , 2008, Molecular & Cellular Proteomics.

[17]  Sung Kyu Park,et al.  A quantitative analysis software tool for mass spectrometry–based proteomics , 2008, Nature Methods.

[18]  Mark D'Ascenzo,et al.  iTRAQPak: an R based analysis and visualization package for 8-plex isobaric protein expression data. , 2008, Briefings in functional genomics & proteomics.

[19]  M. Mann,et al.  Absolute SILAC for accurate quantitation of proteins in complex mixtures down to the attomole level. , 2008, Journal of proteome research.

[20]  E. Izaurralde,et al.  Getting to the Root of miRNA-Mediated Gene Silencing , 2008, Cell.

[21]  R. Aebersold,et al.  Quantitative proteomic analysis to profile dynamic changes in the spatial distribution of cellular proteins. , 2008, Methods in molecular biology.

[22]  Knut Reinert,et al.  OpenMS – An open-source software framework for mass spectrometry , 2008, BMC Bioinformatics.

[23]  Ruedi Aebersold,et al.  The Implications of Proteolytic Background for Shotgun Proteomics*S , 2007, Molecular & Cellular Proteomics.

[24]  M. Mann,et al.  Is Proteomics the New Genomics? , 2007, Cell.

[25]  Patrick G. A. Pedrioli,et al.  A high-quality catalog of the Drosophila melanogaster proteome , 2007, Nature Biotechnology.

[26]  M. Wilm,et al.  Quantitative Proteomics Profiling of Sarcomere Associated Proteins in Limb and Extraocular Muscle Allotypes*S , 2007, Molecular & Cellular Proteomics.

[27]  Yoshiya Oda,et al.  Mass spectrometry-based quantitative proteomics , 2007, Biotechnology & genetic engineering reviews.

[28]  Jun Adachi,et al.  MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes , 2006, Nucleic Acids Res..

[29]  Daniel B. Martin,et al.  Computational prediction of proteotypic peptides for quantitative proteomics , 2007, Nature Biotechnology.

[30]  R. Aebersold,et al.  Using stable isotope tagging and mass spectrometry to characterize protein complexes and to detect changes in their composition. , 2007, Methods in molecular biology.

[31]  M. Mann,et al.  Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks , 2006, Cell.

[32]  M. Mann,et al.  Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK) , 2006, Nature Methods.

[33]  Ronald J. Moore,et al.  More sensitive and quantitative proteomic measurements using very low flow rate porous silica monolithic LC columns with electrospray ionization-mass spectrometry. , 2006, Journal of proteome research.

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

[35]  T. Köcher,et al.  A general precursor ion‐like scanning mode on quadrupole‐TOF instruments compatible with chromatographic separation , 2006, Proteomics.

[36]  Scott J Geromanos,et al.  Quantitative proteomic analysis of drug-induced changes in mycobacteria. , 2006, Journal of proteome research.

[37]  Robertson Craig,et al.  The use of proteotypic peptide libraries for protein identification. , 2005, Rapid communications in mass spectrometry : RCM.

[38]  R. Aebersold,et al.  Scoring proteomes with proteotypic peptide probes , 2005, Nature Reviews Molecular Cell Biology.

[39]  Steven P Gygi,et al.  The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. , 2005, Methods.

[40]  M. Mann,et al.  Quantitative Phosphoproteomics Applied to the Yeast Pheromone Signaling Pathway*S , 2005, Molecular & Cellular Proteomics.

[41]  R. Aebersold,et al.  Increased quantitative proteome coverage with 13C/12C‐based, acid‐cleavable isotope‐coded affinity tag reagent and modified data acquisition scheme , 2005, Proteomics.

[42]  Anthony K. L. Leung,et al.  Nucleolar proteome dynamics , 2005, Nature.

[43]  A. Schmidt,et al.  A novel strategy for quantitative proteomics using isotope‐coded protein labels , 2005, Proteomics.

[44]  Ruedi Aebersold,et al.  Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane , 2004, The Journal of cell biology.

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

[46]  M. Mann,et al.  Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics , 2004, Nature Biotechnology.

[47]  R. Aebersold,et al.  A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A , 2004, Nature Genetics.

[48]  R. Aebersold,et al.  Identification of TFB5, a new component of general transcription and DNA repair factor IIH , 2004, Nature Genetics.

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

[50]  Arun K. Ramani,et al.  Protein interaction networks from yeast to human. , 2004, Current opinion in structural biology.

[51]  B. Kuster,et al.  Femtomol sensitivity post-digest (18)O labeling for relative quantification of differential protein complex composition. , 2004, Rapid communications in mass spectrometry : RCM.

[52]  Waltraud X. Schulze,et al.  A Novel Proteomic Screen for Peptide-Protein Interactions* , 2004, Journal of Biological Chemistry.

[53]  Keqi Tang,et al.  Ultrasensitive and quantitative analyses from combined separations-mass spectrometry for the characterization of proteomes. , 2004, Accounts of chemical research.

[54]  Shu-Hui Chen,et al.  Stable-isotope dimethyl labeling for quantitative proteomics. , 2003, Analytical chemistry.

[55]  P. Bork,et al.  Genome evolution reveals biochemical networks and functional modules , 2003, Proceedings of the National Academy of Sciences of the United States of America.

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

[57]  T. Shaler,et al.  Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. , 2003, Analytical chemistry.

[58]  Xudong Yao,et al.  Trypsin catalyzed 16O-to-18O exchange for comparative proteomics: Tandem mass spectrometry comparison using MALDI-TOF, ESI-QTOF, and ESI-ion trap mass spectrometers , 2003, Journal of the American Society for Mass Spectrometry.

[59]  S. Gygi,et al.  Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[60]  M. Karas,et al.  Effect of different solution flow rates on analyte ion signals in nano-ESI MS, or: when does ESI turn into nano-ESI? , 2003, Journal of the American Society for Mass Spectrometry.

[61]  M. Mann,et al.  Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). , 2003, Journal of proteome research.

[62]  Blagoy Blagoev,et al.  A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling , 2003, Nature Biotechnology.

[63]  Ruedi Aebersold,et al.  The study of macromolecular complexes by quantitative proteomics , 2003, Nature Genetics.

[64]  T. Köcher,et al.  An efficient protein complex purification method for functional proteomics in higher eukaryotes , 2003, Nature Biotechnology.

[65]  M. Mann,et al.  Large-scale Proteomic Analysis of the Human Spliceosome References , 2006 .

[66]  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.

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

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

[69]  M. Mann,et al.  Directed Proteomic Analysis of the Human Nucleolus , 2002, Current Biology.

[70]  S. Gygi,et al.  Toward a high-throughput approach to quantitative proteomic analysis: Expression-dependent protein identification by mass spectrometry , 2001, Journal of the American Society for Mass Spectrometry.

[71]  B. Séraphin,et al.  The tandem affinity purification (TAP) method: a general procedure of protein complex purification. , 2001, Methods.

[72]  Richard D. Smith,et al.  Physical/chemical separations in the break-up of highly charged droplets from electrosprays , 2001, Journal of the American Society for Mass Spectrometry.

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

[74]  R. Knochenmuss,et al.  Secondary ion-molecule reactions in matrix-assisted laser desorption/ionization , 2000, Journal of mass spectrometry : JMS.

[75]  D. Clemmer,et al.  Mobility labeling for parallel CID of ion mixtures. , 2000, Analytical chemistry.

[76]  M Karas,et al.  Ionization in matrix-assisted laser desorption/ionization: singly charged molecular ions are the lucky survivors. , 2000, Journal of mass spectrometry : JMS.

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

[78]  B. Séraphin,et al.  A generic protein purification method for protein complex characterization and proteome exploration , 1999, Nature Biotechnology.

[79]  A. Shevchenko,et al.  Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. , 1996, Analytical chemistry.

[80]  A. Shevchenko,et al.  Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry , 1996, Nature.

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

[82]  M. Wilm,et al.  Error-tolerant identification of peptides in sequence databases by peptide sequence tags. , 1994, Analytical chemistry.

[83]  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.

[84]  M. Wilm,et al.  Electrospray and Taylor-Cone theory, Dole's beam of macromolecules at last? , 1994 .

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

[86]  M. Karas,et al.  Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. , 1988, Analytical chemistry.

[87]  D M Desiderio,et al.  Preparation of stable isotope-incorporated peptide internal standards for field desorption mass spectrometry quantification of peptides in biologic tissue. , 1983, Biomedical mass spectrometry.