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Review

Overcoming the dynamic range problem in mass spectrometry-based shotgun proteomics

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Pages 611-619 | Published online: 09 Jan 2014

References

  • Peng J, Schwartz D, Elias JE et al. A proteomics approach to understanding protein ubiquitination. Nat. Biotechnol.21(8), 921–926 (2003).
  • Ptacek J, Devgan G, Michaud G et al. Global analysis of protein phosphorylation in yeast. Nature438(7068), 679–684 (2005).
  • International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature431(7011), 931–945 (2004).
  • Ghaemmaghami S, Huh WK, Bower K et al. Global analysis of protein expression in yeast. Nature425(6959), 737–741 (2003).
  • Washburn MP, Wolters D, Yates JR 3rd. Large scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol.19(3), 242–247 (2001).
  • de Godoy LM, Olsen JV, de Souza GA et al. Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol.7(6), R50 (2005).
  • Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell Proteomics1(11), 845–867 (2002).
  • Brett D, Pospisil H, Valcarcel J, Reich J, Bork P. Alternative splicing and genome complexity. Nat. Genet.30(1), 29–30 (2002).
  • Modrek B, Resch A, Grasso C, Lee C. Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res.29(13), 2850–2859 (2001).
  • Zimmer JS, Monroe ME, Qian WJ, Smith RD. Advances in proteomics data analysis and display using an accurate mass and time tag approach. Mass Spectrom. Rev.25(3), 450–482 (2006).
  • Kislinger T, Cox B, Kannan A et al. Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell125(1), 173–186 (2006).
  • Mootha VK, Bunkenborg J, Olsen JV et al. Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell115(5), 629–640 (2003).
  • Lipton MS, Pasa-Tolic L, Anderson GA et al. Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc. Natl Acad. Sci. USA99(17), 11049–11054 (2002).
  • Rezaul K, Wu L, Mayya V, Hwang SI, Han D. A systematic characterization of mitochondrial proteome from human T leukemia cells. Mol. Cell Proteomics4(2), 169–181 (2005).
  • Zhou Z, Licklider LJ, Gygi SP, Reed R. Comprehensive proteomic analysis of the human spliceosome. Nature419(6903), 182–185 (2002).
  • Gavin AC, Aloy P, Grandi P et al. Proteome survey reveals modularity of the yeast cell machinery. Nature440(7084), 631–636 (2006).
  • Pasini EM, Kirkegaard M, Mortensen P, Lutz HU, Thomas AW, Mann M. In-depth analysis of the membrane and cytosolic proteome of red blood cells. Blood108(3), 791–801 (2006).
  • O’Farrell PH. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem.250(10), 4007–4021 (1975).
  • Klose J. Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik26(3), 231–243 (1975).
  • Ru QC, Katenhusen RA, Zhu LA et al. Proteomic profiling of human urine using multi-dimensional protein identification technology. J. Chromatogr. A1111(2), 166–174 (2006).
  • Fischer F, Wolters D, Rogner M, Poetsch A. Toward the complete membrane proteome: high coverage of integral membrane proteins through transmembrane peptide detection. Mol. Cell Proteomics5(3), 444–453 (2006).
  • Wu CC, MacCoss MJ, Howell KE, Yates JR 3rd. A method for the comprehensive proteomic analysis of membrane proteins. Nat. Biotechnol.21(5), 532–538 (2003).
  • Gaucher SP, Taylor SW, Fahy E et al. Expanded coverage of the human heart mitochondrial proteome using multidimensional liquid chromatography coupled with tandem mass spectrometry. J. Proteome Res.3(3), 495–505 (2004).
  • Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large scale protein analysis: the yeast proteome. J. Proteome Res.2(1), 43–50 (2003).
  • Nagele E, Vollmer M, Horth P, Vad C. 2D-LC/MS techniques for the identification of proteins in highly complex mixtures. Expert Rev. Proteomics1(1), 37–46 (2004).
  • Motoyama A, Venable JD, Ruse CI, Yates JR 3rd. Automated ultra-high-pressure multidimensional protein identification technology (UHP-MudPIT) for improved peptide identification of proteomic samples. Anal. Chem.78(14), 5109–5118 (2006).
  • Shen Y, Zhang R, Moore RJ et al. Automated 20 kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1000–1500 and capabilities in proteomics and metabolomics. Anal. Chem.77(10), 3090–3100 (2005).
  • Shen Y, Jacobs JM, Camp DG 2nd et al. Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome. Anal. Chem.76(4), 1134–1144 (2004).
  • Shen Y, Zhao R, Berger SJ, Anderson GA, Rodriguez N, Smith RD. High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomics. Anal. Chem.74(16), 4235–4249 (2002).
  • Shen Y, Moore RJ, Zhao R et al. High-efficiency on-line solid-phase extraction coupling to 15–150-microm-i.d. column liquid chromatography for proteomic analysis. Anal. Chem.75(14), 3596–3605 (2003).
  • Schindler J, Lewandrowski U, Sickmann A, Friauf E, Nothwang HG. Proteomic analysis of brain plasma membranes isolated by affinity two-phase partitioning. Mol. Cell Proteomics5(2), 390–400 (2006).
  • Distel B, Kragt A. Purification of yeast peroxisomes. Methods Mol. Biol.313, 21–26 (2006).
  • Pisitkun T, Shen RF, Knepper MA. Identification and proteomic profiling of exosomes in human urine. Proc. Natl Acad. Sci. USA101(36), 13368–13373 (2004).
  • Takatalo MS, Kouvonen P, Corthals G, Nyman TA, Ronnholm RH. Identification of new Golgi complex specific proteins by direct organelle proteomic analysis. Proteomics6(12), 3502–3508 (2006).
  • Andersen JS, Lam YW, Leung AK et al. Nucleolar proteome dynamics. Nature433(7021), 77–83 (2005).
  • Oh P, Li Y, Yu J et al. Subtractive proteomic mapping of the endothelial surface in lung and solid tumors for tissue-specific therapy. Nature429(6992), 629–635 (2004).
  • Blondeau F, Ritter B, Allaire PD et al. Tandem MS analysis of brain clathrin-coated vesicles reveals their critical involvement in synaptic vesicle recycling. Proc. Natl Acad. Sci. USA101(11), 3833–3838 (2004).
  • Ru QC, Zhu LA, Silberman J, Shriver CD. Label-free semiquantitative peptide feature profiling of human breast cancer and breast disease sera via two-dimensional liquid chromatography–mass spectrometry. Mol. Cell Proteomics5(6), 1095–1104 (2006).
  • Echan LA, Tang HY, Ali-Khan N, Lee K, Speicher DW. Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma. Proteomics5(13), 3292–3303 (2005).
  • Huang L, Harvie G, Feitelson JS et al. Immunoaffinity separation of plasma proteins by IgY microbeads: meeting the needs of proteomic sample preparation and analysis. Proteomics5(13), 3314–3328 (2005).
  • Pieper R, Su Q, Gatlin CL, Huang ST, Anderson NL, Steiner S. Multi-component immunoaffinity subtraction chromatography: an innovative step towards a comprehensive survey of the human plasma proteome. Proteomics3(4), 422–432 (2003).
  • Gong Y, Li X, Yang B et al. Different immunoaffinity fractionation strategies to characterize the human plasma proteome. J. Proteome Res.5(6), 1379–1387 (2006).
  • Brand J, Haslberger T, Zolg W, Pestlin G, Palme S. Depletion efficiency and recovery of trace markers from a multiparameter immunodepletion column. Proteomics6(11), 3236–3242 (2006).
  • Blagoev B, Ong SE, Kratchmarova I, Mann M. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat. Biotechnol.22(9), 1139–1145 (2004).
  • Beausoleil SA, Jedrychowski M, Schwartz D et al. Large scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl Acad. Sci. USA101(33), 12130–12135 (2004).
  • Ficarro SB, McCleland ML, Stukenberg PT et al. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae.Nat. Biotechnol.20(3), 301–305 (2002).
  • Moser K, White FM. Phosphoproteomic analysis of rat liver by high capacity IMAC and LC-MS/MS. J. Proteome Res.5(1), 98–104 (2006).
  • Larsen MR, Thingholm TE, Jensen ON, Roepstorff P, Jorgensen TJ. Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol. Cell Proteomics4(7), 873–886 (2005).
  • Ludwig JA, Weinstein JN. Biomarkers in cancer staging, prognosis and treatment selection. Nat. Rev. Cancer5(11), 845–856 (2005).
  • Lolli F, Rovero P, Chelli M, Papini AM. Toward biomarkers in multiple sclerosis: new advances. Expert Rev. Neurother.6(5), 781–794 (2006).
  • Kaji H, Saito H, Yamauchi Y et al. Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins. Nat. Biotechnol.21(6), 667–672 (2003).
  • Yang Z, Hancock WS, Chew TR, Bonilla L. A study of glycoproteins in human serum and plasma reference standards (HUPO) using multilectin affinity chromatography coupled with RPLC-MS/MS. Proteomics5(13), 3353–3366 (2005).
  • Zhang H, Li XJ, Martin DB, Aebersold R. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat. Biotechnol.21(6), 660–666 (2003).
  • Mayya V, Rezaul K, Cong YS, Han D. Systematic comparison of a two-dimensional ion trap and a three-dimensional ion trap mass spectrometer in proteomics. Mol. Cell Proteomics4(2), 214–223 (2005).
  • Foster LJ, de Hoog CL, Zhang Y, Xie X, Mootha VK, Mann M. A mammalian organelle map by protein correlation profiling. Cell125(1), 187–199 (2006).
  • Chen EI, Hewel J, Felding-Habermann B, Yates JR 3rd. Large scale protein profiling by combination of protein fractionation and multidimensional protein identification technology (MudPIT). Mol. Cell Proteomics5(1), 53–56 (2006).
  • Elias JE, Haas W, Faherty BK, Gygi SP. Comparative evaluation of mass spectrometry platforms used in large scale proteomics investigations. Nat. Methods2(9), 667–675 (2005).
  • Zheng X, Baker H, Hancock WS. Analysis of the low molecular weight serum peptidome using ultrafiltration and a hybrid ion trap–Fourier transform mass spectrometer. J. Chromatogr. A.1120(1–2), 173–184 (2006).
  • Olsen JV, Mann M. Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc. Natl Acad. Sci. USA101(37), 13417–13422 (2004).
  • Hardman M, Makarov AA. Interfacing the orbitrap mass analyzer to an electrospray ion source. Anal. Chem.75(7), 1699–1705 (2003).
  • Makarov A, Denisov E, Kholomeev A et al. Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal. Chem.78(7), 2113–2120 (2006).
  • Yates JR, Cociorva D, Liao L, Zabrouskov V. Performance of a linear ion trap-orbitrap hybrid for peptide analysis. Anal. Chem.78(2), 493–500 (2006).
  • Liu H, Sadygov RG, Yates JR 3rd. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem.76(14), 4193–4201 (2004).
  • Hwang SI, Thumar J, Lundgren DH et al. Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues. Oncogene (2006) (Epub ahead of print).
  • Kuhn E, Wu J, Karl J, Liao H, Zolg W, Guild B. Quantification of C-reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C-labeled peptide standards. Proteomics4(4), 1175–1186 (2004).
  • Barnidge DR, Goodmanson MK, Klee GG, Muddiman DC. Absolute quantification of the model biomarker prostate-specific antigen in serum by LC-Ms/MS using protein cleavage and isotope dilution mass spectrometry. J. Proteome Res.3(3), 644–652 (2004).
  • Wu SL, Amato H, Biringer R, Choudhary G, Shieh P, Hancock WS. Targeted proteomics of low-level proteins in human plasma by LC/MSn: using human growth hormone as a model system. J. Proteome Res.1(5), 459–465 (2002).
  • Unwin RD, Griffiths JR, Leverentz MK, Grallert A, Hagan IM, Whetton AD. Multiple reaction monitoring to identify sites of protein phosphorylation with high sensitivity. Mol. Cell Proteomics4(8), 1134–1144 (2005).
  • Lin S, Shaler TA, Becker CH. Quantification of intermediate-abundance proteins in serum by multiple reaction monitoring mass spectrometry in a single-quadrupole ion trap. Anal. Chem.78(16), 5762–5767 (2006).
  • Anderson L, Hunter CL. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell Proteomics5(4), 573–588 (2006).
  • Mayya V, Rezual K, Wu L, Fong MB, Han DK. Absolute quantification of multisite phosphorylation by selective reaction monitoring mass spectrometry: determination of inhibitory phosphorylation status of cyclin-dependent kinases. Mol. Cell Proteomics5(6), 1146–1157 (2006).
  • Anderson NL, Anderson NG, Haines LR, Hardie DB, Olafson RW, Pearson TW. Mass spectrometric quantitation of peptides and proteins using stable isotope standards and capture by anti-peptide antibodies (SISCAPA). J. Proteome Res.3(2), 235–244 (2004).
  • Cutillas PR, Khwaja A, Graupera M et al. Ultrasensitive and absolute quantification of the phosphoinositide-3 kinase/Akt signal transduction pathway by mass spectrometry. Proc. Natl Acad. Sci. USA103(24), 8959–8964 (2006).
  • Eng J, McCormack AL, Yates JR 3rd. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom.5, 976–989 (1994).
  • Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis20(18), 3551–3567 (1999).
  • Tanner S, Shu H, Frank A et al. InsPecT: identification of post-translationally modified peptides from tandem mass spectra. Anal. Chem.77(14), 4626–4639 (2005).
  • Zhang N, Li XJ, Ye M, Pan S, Schwikowski B, Aebersold R. ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer. Proteomics5(16), 4096–4106 (2005).
  • Higdon R, Hogan JM, Van Belle G, Kolker E. Randomized sequence databases for tandem mass spectrometry peptide and protein identification. Omics9(4), 364–379 (2005).
  • Reddy AB, Karp NA, Maywood ES et al. Circadian orchestration of the hepatic proteome. Curr. Biol.16(11), 1107–1115 (2006).
  • Forner F, Foster LJ, Campanaro S, Valle G, Mann M. Quantitative proteomic comparison of rat mitochondria from muscle, heart, and liver. Mol. Cell Proteomics5(4), 608–619 (2006).
  • Krogan NJ, Cagney G, Yu H et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature440(7084), 637–643 (2006).
  • Fermin D, Allen BB, Blackwell TW et al. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol.7(4), R35 (2006).
  • Kalume DE, Peri S, Reddy R et al. Genome annotation of Anopheles gambiae using mass spectrometry-derived data. BMC Genomics6, 128 (2005).
  • Xia Q, Hendrickson EL, Zhang Y et al. Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR. Mol. Cell Proteomics5(5), 868–881 (2006).
  • Olsen JV, Blagoev B, Gnad F, et al. Global, In vivo, and site-specific phosphorylation dynamics in signaling networks. Cell127(3), 635–648 (2006).

Website

  • Association of Biomolecular Resource Facilities www.abrf.org/index.cfm/dm.home?AvgMass=all (Accessed August 2006)

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