Mass spectrometry-based peptide quantification: applications and limitations

References

• Pandey A, Mann M. Proteomics to study genes and genomes. Nature 405, 837–846 (2000).
   PubMed Web of Science ®Google Scholar
• Moseley MA. Current trends in differential expression proteomics: isotopically coded tags. Trends Biotechnol. 19, S10–S16 (2001).
   Google Scholar
• Monteoliva L, Albar JP. Differential proteomics: an overview of gel and non-gel based approaches. Brief. Funct. Genomic Proteomic 3, 220–239 (2004).
   PubMedGoogle Scholar
• Hegde PS, White IR, Debouck C. Interplay of transcriptomics and proteomics. Curr. Opin. Biotechnol. 14, 647–51 (2003).
   PubMed Web of Science ®Google Scholar
• O’Farrell PH. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250, 4007–4021 (1975).
   PubMed Web of Science ®Google Scholar
• Klose J. Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 26, 231–243 (1975).
   PubMedGoogle Scholar
• Unlu M, Morgan ME, Minden JS. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18, 2071–2077 (1997).
   PubMed Web of Science ®Google Scholar
• Von Eggeling F, Gawriljuk A, Fiedler W et al. Fluorescent dual colour 2D-protein gel electrophoresis for rapid detection of differences in protein pattern with standard image analysis software. Int. J. Mol. Med. 8, 373–377 (2001).
   PubMedGoogle Scholar
• Tonge R, Shaw J, Middleton B et al. Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 1, 377–396 (2001).
   PubMed Web of Science ®Google Scholar
• Yan JX, Devenish AT, Wait R et al. Fluorescence two-dimensional difference gel electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli. Proteomics 2, 1682–1698 (2002).
   PubMed Web of Science ®Google Scholar
• Görg A, Weiss W, Dunn MJ. Current two-dimensional electrophoresis technology for proteomics. Proteomics 4, 3665–3685 (2004).
   PubMed Web of Science ®Google Scholar
• Church S. Advances in two-dimensional gel matching technology. Biochem. Soc. Trans. 32, 511–5116 (2004).
   PubMedGoogle Scholar
• Dowsey AW, Dunn MJ, Yang GZ. The role of bioinformatics in 2D gel electrophoresis. Proteomics 3, 1567–1596 (2003).
   PubMed Web of Science ®Google Scholar
• Hamdan M, Righetti PG. Modern strategies for protein quantification in proteome analysis: advantages and limitations. Mass Spectrom. Rev. 21, 287–302 (2002).
   PubMed Web of Science ®Google Scholar
• Goodlett DR, Keller A, Watts JD et al. Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation. Rapid Commun. Mass Spectrom. 15, 1214–1221 (2001).
   PubMed Web of Science ®Google Scholar
• Wagner Y, Sickmann A, Meyer HE, Daum G. Multidimensional nano-HPLC for analysis of protein complexes. J. Am. Soc. Mass Spectrom. 14, 1003–1011 (2003).
   PubMed Web of Science ®Google Scholar
• Andersen JS, Wilkinson CJ, Mayor T et al. Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426, 570–574 (2003).
   PubMed Web of Science ®Google Scholar
• Wiener MC, Sachs JR, Deyanova EG, Yates NA. Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures. Anal. Chem. 76, 6085–6096 (2004).
   PubMed Web of Science ®Google Scholar
• Steen H, Jebanathirajah JA, Springer M, Kirschner MW. Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MS. Proc. Natl Acad. Sci. USA 102, 3948–3953 (2005).
   PubMed Web of Science ®Google Scholar
• Cagney G, Emili A. De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging. Nature Biotechnol. 20, 163–170 (2002).
   PubMed Web of Science ®Google Scholar
• Watt SA, Patschkowski T, Kalinowski J, Niehaus K. Qualitative and quantitative proteomics by two-dimensional gel electrophoresis, peptide mass fingerprint and a chemically-coded affinity tag (CCAT). J. Biotechnol. 106, 287–300 (2003).
   PubMed Web of Science ®Google Scholar
• Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 422, 198–207 (2003).
   PubMed Web of Science ®Google Scholar
• Aebersold R, Goodlett DR. Mass spectrometry in proteomics. Chem. Rev. 101, 269–295 (2001).
   PubMed Web of Science ®Google Scholar
• Reinders J, Lewandrowski U, Moebius J, Wagner Y, Sickmann A. Challenges in mass spectrometry-based proteomics. Proteomics 4, 3686–3703 (2004).
   PubMed Web of Science ®Google Scholar
• Lee YH, Han H, Chang SB, Lee SW. Isotope-coded N-terminal sulfonation of peptides allows quantitative proteomic analysis with increased de novo peptide sequencing capability. Rapid Commun. Mass Spectrom. 18, 3019–3027 (2004).
   PubMedGoogle Scholar
• Cargile BJ, Bundy LJ, Grunden AM, Stephenson JL Jr. Synthesis/degradation ratio mass spectrometry for measuring relative dynamic protein turnover. Anal. Chem. 76, 86–97 (2004).
   PubMed Web of Science ®Google Scholar
• Mitulovic G, Stingl C, Smoluch M et al. Automated, on-line two-dimensional nano liquid chromatography tandem mass spectrometry for rapid analysis of complex protein digests. Proteomics 4, 2545–2557 (2004).
   PubMed Web of Science ®Google Scholar
• Mitulovic G, Smoluch M, Chervet JP et al. An improved method for tracking and reducing the void volume in nano HPLC-MS with micro trapping columns. Anal. Bioanal. Chem. 376, 946–951 (2003).
   PubMed Web of Science ®Google Scholar
• Wolters DA, Washburn MP, Yates JR III. An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73, 5683–5690 (2001).
   PubMed Web of Science ®Google Scholar
• Hansen KC, Schmitt-Ulms G, Chalkley RJ et al. Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotope-coded affinity tag and multidimensional chromatography. Mol. Cell. Proteomics 2, 299–314 (2003).
   PubMed Web of Science ®Google Scholar
• Oda Y, Owa T, Sato T et al. Quantitative chemical proteomics for identifying candidate drug targets. Anal. Chem. 75, 2159–2165 (2003).
   PubMed Web of Science ®Google Scholar
• Moritz B, Meyer HE. Approaches for the quantification of protein concentration ratios. Proteomics 3, 2208–2220 (2003).
   PubMedGoogle Scholar
• Gygi SP, Rist B, Gerber SA et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnol. 17, 994–999 (1999).
   PubMed Web of Science ®Google Scholar
• Andersen JS, Lam YW, Leung AKJ et al. Nucleolar proteome dynamics. Nature 433, 77–83 (2005).
   PubMed Web of Science ®Google Scholar
• Ong S, Blagoev B, Kratchmarovat I et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1.5, 376–386 (2002).
   PubMedGoogle Scholar
• Ong S, Kratchmarova I, Mann M. Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J. Proteome Res. 2, 173–181 (2003).
   PubMed Web of Science ®Google Scholar
• Blagoev B, Kratchmarova I, Ong S et al. A proteomics strategy to elucidate functional protein–protein interactions applied to EGF signaling. Nature Biotechnol. 21, 315–318 (2003).
   PubMed Web of Science ®Google Scholar
• Everley PA, Krijgsveld J, Zetter BR, Gygi SP. Quantitative cancer proteomics: stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research. Mol. Cell. Proteomics 3, 729–735 (2004).
   PubMed Web of Science ®Google Scholar
• Blagoev B, Ong SE, Kratchmarova I, Mann M. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nature Biotechnol. 22, 1139–1145 (2004).
   PubMed Web of Science ®Google Scholar
• Jiang H, English AM. Quantitative analysis of the yeast proteome by incorporation of isotopically labeled leucine. J. Proteome Res. 1, 345–350 (2002).
   PubMed Web of Science ®Google Scholar
• Zhu H, Pan S, Gu S, Bradbury EM, Chen X. Amino acid residue specific stable isotope labeling for quantitative proteomics. Rapid Commun. Mass Spectrom. 16, 2115–2123 (2002).
   PubMed Web of Science ®Google Scholar
• MacCoss MJ, Wu CC, Liu H, Sadygov R, Yates JR III. A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal. Chem. 75, 6912–6921 (2003).
   PubMed Web of Science ®Google Scholar
• Li XJ, Zhang H, Ranish JA, Aebersold R. Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal. Chem. 75, 6648–6657 (2003).
   PubMed Web of Science ®Google Scholar
• Krijgsveld J, Ketting RF, Mahmoudi T et al. Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nature Biotechnol. 21, 927–931 (2003).
   PubMed Web of Science ®Google Scholar
• Kohno T, Kusunoki H, Sato K, Wakamatsu K. A new general method for the biosynthesis of stable isotope-enriched peptides using a decahistidine-tagged ubiquitin fusion system: an application to the production of mastoparan-X uniformly enriched with 15N and 15N/13C. J. Biomol. NMR 12, 109–121 (1998).
   PubMed Web of Science ®Google Scholar
• Washburn MP, Ulaszek R, Deciu C, Schieltz DM, Yates JR III. Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal. Chem. 74, 1650–1657 (2002).
   PubMed Web of Science ®Google Scholar
• Pasa-Tolic L, Jensen PK, Anderson GA et al. High throughput proteome-wide precision measurements of protein expression using mass spectrometry. J. Am. Chem. Soc. 121, 7949–7950 (1999).
   Web of Science ®Google Scholar
• Oda Y, Huang K, Cross FR, Cowburn D, Chait BT. Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl Acad. Sci. USA 96, 6591–6596 (1999).
   PubMed Web of Science ®Google Scholar
• Ross PL, Huang YN, Marchese JN et al. Multiplexed protein quantitation in saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3, 1154–1169 (2004).
   PubMed Web of Science ®Google Scholar
• Smolka MB, Zhou H, Purkayastha S, Aebersold R. Optimization of the isotope-coded affinity tag-labeling procedure for quantitative proteome analysis. Anal. Biochem. 297, 25–31 (2001).
   PubMed Web of Science ®Google Scholar
• Dunkley TP, Watson R, Griffin JL, Dupree P, Lilley KS. Localization of organelle proteins by isotope tagging (LOPIT). Mol. Cell. Proteomics 3, 1128–34 (2004).
   PubMed Web of Science ®Google Scholar
• Dunkley TP, Dupree P, Watson RB, Lilley KS. The use of isotope-coded affinity tags (ICAT) to study organelle proteomes in Arabidopsis thaliana. Biochem. Soc. Trans. 32, 520–523 (2004).
   PubMed Web of Science ®Google Scholar
• Gygi SP, Rist B, Griffin TJ, Eng J, Aebersold R. Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. J. Proteome Res. 1, 47–54 (2002).
   PubMed Web of Science ®Google Scholar
• Yi EC, Li XJ, Cooke K et al. Increased quantitative proteome coverage with 13C/12C-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme. Proteomics 5(2), 380–387 (2005).
   PubMed Web of Science ®Google Scholar
• Stewart T II, Thomson, Figeys D. 18O labeling: a tool for proteomics. Rapid Commun. Mass Spectrom. 15, 2456–65 (2001).
   PubMed Web of Science ®Google Scholar
• Heller M, Mattou H, Menzel C, Yao X. Trypsin catalyzed 16O-to-18O exchange for comparative proteomics: tandem mass spectrometry comparison using MALDI-TOF, ESI-QTOF, and ESI-ion trap mass spectrometers. J. Am. Soc. Mass Spectrom. 14, 704–718 (2003).
   PubMed Web of Science ®Google Scholar
• Schnölzer M, Jedrzejewski P, Lehmann WD. Protease-catalyzed incorporation of 18O into peptide fragments and its application for protein sequencing by electrospray and matrix-assisted laser desorption/ionization mass spectrometry. Electrophoresis 17, 945–953 (1996).
   PubMed Web of Science ®Google Scholar
• Yao X, Freas A, Ramirez J, Demirev PA, Fenselau C. Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal. Chem. 73, 2836–2842 (2001).
   PubMed Web of Science ®Google Scholar
• Chakraborty A, Regnier FE. Global internal standard technology for comparative proteomics. J. Chromatogr. A. 949, 173–184 (2002).
   PubMed Web of Science ®Google Scholar
• Geng M, Ji J, Regnier FE. Signature-peptide approach to detecting proteins in complex mixtures. J. Chromatogr. A 870, 295–313 (2000).
   PubMed Web of Science ®Google Scholar
• Ji J, Chakraborty A, Geng M et al. Strategy for qualitative and quantitative analysis in proteomics based on signature peptides. J. Chromatogr. B Biomed. Sci. Appl. 745, 197–210 (2000).
   PubMed Web of Science ®Google Scholar
• Schmidt A, Kellermann J, Lottspeich F. A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5(1), 4–15 (2005).
   PubMed Web of Science ®Google Scholar
• Brönstrup M. Absolute quantification strategies in proteomics based on mass spectrometry. Expert Rev. Proteomics. 1, 503–512 (2004).
   PubMed Web of Science ®Google Scholar
• Hochleitner EO, Kastner B, Frohlich T et al. Protein stoichiometry of a multi-protein complex, the human spliceosomal U1 small nuclear ribonucleoprotein: absolute quantification using isotope-coded tags and mass spectrometry. J. Biol. Chem. 280, 2536–2542 (2005).
   PubMed Web of Science ®Google Scholar
• Hsu JL, Huang SY, Shiea JT, Huang WY, Chen SH. Beyond quantitative proteomics: signal enhancement of the a(1) ion as a mass tag for peptide sequencing using dimethyl labeling. J. Proteome Res. 4, 101–108 (2005).
   PubMedGoogle Scholar
• Potthast F, Ocenasek J, Rutishauser D, Pelikan M, Schlapbach R. Database independent detection of isotopically labeled MS/MS spectrum peptide pairs. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 817, 225–230 (2005).
   PubMedGoogle Scholar
• Flensburg J, Haid D, Blomberg J, Bielawski J, Ivansson D. Applications and performance of a MALDI-ToF mass spectrometer with quadratic field reflectron technology. J. Biochem. Biophys. Methods 60, 319–334 (2004).
   PubMedGoogle Scholar
• Keough T, Lacey MP, Youngquist RS. Derivatization procedures to facilitate de novo sequencing of lysine-terminated tryptic peptides using postsource decay matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 14, 2348–56 (2000).
   PubMed Web of Science ®Google Scholar
• Conrads TP, Alving K, Veenstra TD et al. Quantitative analysis of bacterial and mammalian proteomes using a combination of cysteine affinity tags and 15N-metabolic labeling. Anal. Chem. 73, 2132–2139 (2001).
   PubMed Web of Science ®Google Scholar
• Heck AJR, Krijgsveld J. Mass spectrometry-based quantitative proteomics. Expert Rev. Proteomics 1, 317–326 (2004).
   PubMed Web of Science ®Google Scholar
• Qian W-J, Camp D, Smith R. High-throughput proteomics using Fourier transform ion cyclotron resonance mass spectrometry. Expert Rev. Proteomics 1, 87–95 (2004).
   PubMed Web of Science ®Google Scholar
• Wu CC, MacCoss MJ, Howell KE, Matthews DE, Yates JR III. Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis. Anal. Chem. 76, 4951–4959 (2004).
   PubMed Web of Science ®Google Scholar
• van Rooijen N. Labelling of lymphocytes with various radiosotopes for in vivo tracer studies; a review. J. Immunol. Methods 15, 267–277 (1977).
   PubMedGoogle Scholar
• Humphrey TJ, Davies DD. A new method for the measurement of protein turnover. Biochem. J. 148, 119–127 (1975).
   PubMedGoogle Scholar
• Kolkman A, Dirksen EH, Slijper M, Heck AJ. Double standards in quantitative proteomics: direct comparative assessment of difference in gel electrophoresis (DiGE) and metabolic stable isotope labeling. Mol. Cell. Proteomics 4(3), 255–266 (2005).
   PubMedGoogle Scholar