3,624
Views
102
CrossRef citations to date
0
Altmetric
Theme: Biomarker Diagnostics - Reviews

Mass spectrometric protein maps for biomarker discovery and clinical research

, , &
Pages 811-825 | Published online: 09 Jan 2014

References

  • Etzioni R, Urban N, Ramsey S et al. The case for early detection. Nat. Rev. Cancer 3(4), 243–252 (2003).
  • Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol. 24(8), 971–983 (2006).
  • Sawyers CL. The cancer biomarker problem. Nature 452(7187), 548–552 (2008).
  • Sobin LH. TNM: evolution and relation to other prognostic factors. Semin. Surg. Oncol. 21(1), 3–7 (2003).
  • Hamburg MA, Collins FS. The path to personalized medicine. N. Engl. J. Med. 363(4), 301–304 (2010).
  • Aebersold R, Anderson L, Caprioli R, Druker B, Hartwell L, Smith R. Perspective: a program to improve protein biomarker discovery for cancer. J. Proteome Res. 4(4), 1104–1109 (2005).
  • Domon B, Aebersold R. Options and considerations when selecting a quantitative proteomics strategy. Nat. Biotechnol. 28(7), 710–721 (2010).
  • Picotti P, Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat. Methods 9(6), 555–566 (2012).
  • Picotti P, Bodenmiller B, Aebersold R. Proteomics meets the scientific method. Nat. Methods 10(1), 24–27 (2013).
  • Huttenhain R, Soste M, Selevsek N et al. Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Sci. Transl. Med. 4(142), 142ra194 (2012).
  • Kalin M, Cima I, Schiess R et al. Novel prognostic markers in the serum of patients with castration-resistant prostate cancer derived from quantitative analysis of the pten conditional knockout mouse proteome. Eur. Urol. 60(6), 1235–1243 (2011).
  • Cima I, Schiess R, Wild P et al. Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer. Proc. Natl Acad. Sci. USA 108(8), 3342–3347 (2011).
  • Gillet LC, Navarro P, Tate S et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell. Proteomics 11(6), O111 016717 (2012).
  • Reiter L, Rinner O, Picotti P et al. mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat. Methods 8(5), 430–435 (2011).
  • Diamandis EP. The failure of protein cancer biomarkers to reach the clinic: why, and what can be done to address the problem? BMC Med. 10, 87 (2012).
  • Addona TA, Abbatiello SE, Schilling B et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotechnol. 27(7), 633–641 (2009).
  • Roobol MJ, Carlsson SV. Risk stratification in prostate cancer screening. Nat. Rev. Urol. 10(1), 38–48 (2013).
  • Karam AK, Karlan BY. Ovarian cancer: the duplicity of CA125 measurement. Nat. Rev. Clin. Oncol. 7(6), 335–339 (2010).
  • Del Mastro L, Lambertini M, Bighin C et al. Trastuzumab as first-line therapy in HER2-positive metastatic breast cancer patients. Expert Rev. Anticancer Ther. 12(11), 1391–1405 (2012).
  • Domon B, Aebersold R. Mass spectrometry and protein analysis. Science 312(5771), 212–217 (2006).
  • Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 422(6928), 198–207 (2003).
  • Sabido E, Selevsek N, Aebersold R. Mass spectrometry-based proteomics for systems biology. Curr. Opin. Biotechnol. 23(4), 591–597 (2012).
  • Elias JE, Gygi SP. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4(3), 207–214 (2007).
  • Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnology 26(12), 1367–1372 (2008).
  • Tabb DL, Vega-Montoto L, Rudnick PA et al. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J. Proteome Res. 9(2), 761–776 (2010).
  • Kim YJ, Feild B, Fitzhugh W et al. Reference map for liquid chromatography-mass spectrometry-based quantitative proteomics. Anal Biochem. 393(2), 155–162 (2009).
  • Schmidt A, Gehlenborg N, Bodenmiller B et al. An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures. Mol. Cell. Proteomics 7(11), 2138–2150 (2008).
  • Jaffe JD, Keshishian H, Chang B, Addona TA, Gillette MA, Carr SA. Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification. Mol. Cell. Proteomics 7(10), 1952–1962 (2008).
  • Peterson AC, Russell JD, Bailey DJ, Westphall MS, Coon JJ. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol. Cell. Proteomics 11(11), 1475–1488 (2012).
  • Lange V, Picotti P, Domon B, Aebersold R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol. Syst. Biol. 4, 222 (2008).
  • Nilsson T, Mann M, Aebersold R, Yates JR 3rd, Bairoch A, Bergeron JJ. Mass spectrometry in high-throughput proteomics: ready for the big time. Nat. Methods 7(9), 681–685 (2010).
  • Lam H, Deutsch EW, Eddes JS, Eng JK, Stein SE, Aebersold R. Building consensus spectral libraries for peptide identification in proteomics. Nat. Methods 5(10), 873–875 (2008).
  • Lam H, Aebersold R. Spectral library searching for peptide identification via tandem MS. Methods Mol. Biol. 604, 95–103 (2010).
  • Lam H, Deutsch EW, Eddes JS et al. Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7(5), 655–667 (2007).
  • Picotti P, Clement-Ziza M, Lam H et al. A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature 494(7436), 266–270 (2013).
  • Deutsch EW, Lam H, Aebersold R. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 9(5), 429–434 (2008).
  • Frank R. The SPOT-synthesis technique. Synthetic peptide arrays on membrane supports--principles and applications. J. Immunol. Methods 267(1), 13–26 (2002).
  • Picotti P, Rinner O, Stallmach R et al. High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat. Methods 7(1), 43–46 (2010).
  • Ahrens CH, Brunner E, Qeli E, Basler K, Aebersold R. Generating and navigating proteome maps using mass spectrometry. Nat. Rev. Mol. Cell Biol. 11(11), 789–801 (2010).
  • Karlsson C, Malmstrom L, Aebersold R, Malmstrom J. Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes. Nat. Commun. 3, 1301 (2012).
  • Schubert OT, Mouritsen J, Ludwig C et al. The Mtb Proteome Library: A Resource of Assays to Quantify the Complete Proteome of Mycobacterium tuberculosis. Cell Host Microbe 13(5), 602–612 (2013).
  • Desiere F, Deutsch EW, King NL et al. The PeptideAtlas project. Nucleic Acids Res. 34(Database issue), D655–D658 (2006).
  • Mathivanan S, Ahmed M, Ahn NG et al. Human Proteinpedia enables sharing of human protein data. Nat. Biotechnol. 26(2), 164–167 (2008).
  • Craig R, Cortens JP, Beavis RC. Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res. 3(6), 1234–1242 (2004).
  • Jones P, Cote RG, Cho SY et al. PRIDE: new developments and new datasets. Nucleic Acids Res. 36(Database issue), D878–D883 (2008).
  • Farrah T, Deutsch EW, Kreisberg R et al. PASSEL: the Pepti deAtlas SRM experiment library. Proteomics 12(8), 1170–1175 (2012).
  • Zhang H, Liu AY, Loriaux P et al. Mass spectrometric detection of tissue proteins in plasma. Mol. Cell. Proteomics 6(1), 64–71 (2007).
  • Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics 1(11), 845–867 (2002).
  • States DJ, Omenn GS, Blackwell TW et al. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat. Biotechnol 24(3), 333–338 (2006).
  • Farrah T, Deutsch EW, Omenn GS et al. A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol. Cell. Proteomics 10(9), M110 006353 (2011).
  • Taussig MJ, Stoevesandt O, Borrebaeck CA et al. ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nat. Methods 4(1), 13–17 (2007).
  • Lundberg E, Fagerberg L, Klevebring D et al. Defining the transcriptome and proteome in three functionally different human cell lines. Mol. Syst. Biol. 6, 450 (2010).
  • Mann M, Kulak NA, Nagaraj N, Cox J. The coming age of complete, accurate, and ubiquitous proteomes. Mol. Cell 49(4), 583–590 (2013).
  • Nagaraj N, Wisniewski JR, Geiger T et al. Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Syst. Biol. 7, 548 (2011).
  • Beck M, Schmidt A, Malmstroem J et al. The quantitative proteome of a human cell line. Mol. Syst. Biol. 7, 549 (2011).
  • Wisniewski JR, Ostasiewicz P, Dus K, Zielinska DF, Gnad F, Mann M. Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma. Mol. Syst. Biol. 8, 611 (2012).
  • Fagerberg L, Oksvold P, Skogs M et al. Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP). J. Proteome Res. (2012).
  • Farrah T, Deutsch EW, Hoopmann MR et al. The state of the human proteome in 2012 as viewed through PeptideAtlas. J. Proteome Res. 12(1), 162–171 (2013).
  • Polanski M, Anderson NL. A list of candidate cancer biomarkers for targeted proteomics. Biomarker insights 1, 1–48 (2007).
  • Wollscheid B, Bausch-Fluck D, Henderson C et al. Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat. Biotechnol. 27(4), 378–386 (2009).
  • Roth J. Protein N-glycosylation along the secretory pathway: relationship to organelle topography and function, protein quality control, and cell interactions. Chem. Rev. 102(2), 285–303 (2002).
  • Schiess R, Wollscheid B, Aebersold R. Targeted proteomic strategy for clinical biomarker discovery. Mol. Oncol. 3(1), 33–44 (2009).
  • 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).
  • Zielinska DF, Gnad F, Wisniewski JR, Mann M. Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints. Cell 141(5), 897–907 (2010).
  • Tian Y, Bova GS, Zhang H. Quantitative glycoproteomic analysis of optimal cutting temperature-embedded frozen tissues identifying glycoproteins associated with aggressive prostate cancer. Anal Chem. 83(18), 7013–7019 (2011).
  • Chen R, Tan Y, Wang M et al. Development of glycoprotein capture-based label-free method for the high-throughput screening of differential glycoproteins in hepatocellular carcinoma. Mol. Cell. Proteomics 10(7), M110 006445 (2011).
  • Zeng X, Hood BL, Sun M et al. Lung cancer serum biomarker discovery using glycoprotein capture and liquid chromatography mass spectrometry. J. Proteome Res. 9(12), 6440–6449 (2010).
  • Huttenhain R, Surinova S, Ossola R et al. N-Glycoprotein SRMAtlas: a resource of mass-spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications. Mol. Cell. Proteomics 12(4), 1005–1016 (2013).
  • Michalski A, Damoc E, Lange O et al. 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(3), O111 013698 (2012).
  • Cristobal A, Hennrich ML, Giansanti P, Goerdayal SS, Heck AJ, Mohammed S. In-house construction of a UHPLC system enabling the identification of over 4000 protein groups in a single analysis. Analyst 137(15), 3541–3548 (2012).
  • Wu L, Han DK. Overcoming the dynamic range problem in mass spectrometry-based shotgun proteomics. Expert Rev. Proteomics 3(6), 611–619 (2006).
  • Schmidt A, Claassen M, Aebersold R. Directed mass spectrometry: towards hypothesis-driven proteomics. Curr. Opin. Chem. Biol. 13(5–6), 510–517 (2009).
  • Liu YS, Luo XY, Li QR et al. Shotgun and targeted proteomics reveal that pre-surgery serum levels of LRG1, SAA, and C4BP may refine prognosis of resected squamous cell lung cancer. J. Mol. Cell Biol. 4(5), 344–347 (2012).
  • Kuzyk MA, Smith D, Yang J et al. Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma. Mol. Cellular Proteomics 8(8), 1860–1877 (2009).
  • Surinova S, Schiess R, Huttenhain R, Cerciello F, Wollscheid B, Aebersold R. On the development of plasma protein biomarkers. J. Proteome Res. 10(1), 5–16 (2011).
  • Huttenhain R, Malmstrom J, Picotti P, Aebersold R. Perspectives of targeted mass spectrometry for protein biomarker verification. Current Opin. Chem. Biol. 13(5–6), 518–525 (2009).
  • Stahl-Zeng J, Lange V, Ossola R et al. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol. Cell. Proteomics 6(10), 1809–1817 (2007).
  • Selevsek N, Matondo M, Sanchez Carbayo M, Aebersold R, Domon B. Systematic quantification of peptides/proteins in urine using selected reaction monitoring. Proteomics 11(6), 1135–1147 (2011).
  • Ebhardt HA, Sabido E, Huttenhain R, Collins B, Aebersold R. Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate. Proteomics 12(8), 1185–1193 (2012).
  • 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 A ntibodies (SISCAPA). J. Proteome Res. 3(2), 235–244 (2004).
  • Whiteaker JR, Zhao L, Anderson L, Paulovich AG. An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers. Mol. Cell. Proteomics 9(1), 184–196 (2010).
  • Kuhn E, Addona T, Keshishian H et al. Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry. Clin. Chem. 55(6), 1108–1117 (2009).
  • Kuhn E, Whiteaker JR, Mani DR et al. Interlaboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma. Mol. Cell. Proteomics 11(6), M111 013854 (2012).
  • Liu Y, Huttenhain R, Surinova S et al. Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS. Proteomics 13(8), 1247–1256 (2013).
  • Wang Q, Chaerkady R, Wu J et al. Mutant proteins as cancer-specific biomarkers. Proc. Natl Acad. Sci. USA 108(6), 2444–2449 (2011).
  • Makridakis M, Vlahou A. Secretome proteomics for discovery of cancer biomarkers. J. Proteomics 73(12), 2291–2305 (2010).
  • Luo X, Liu Y, Wang R, Hu H, Zeng R, Chen H. A high-quality secretome of A549 cells aided the discovery of C4b-binding protein as a novel serum biomarker for non-small cell lung cancer. J. Proteomics 74(4), 528–538 (2011).
  • Liu Y, Luo X, Hu H et al. Integrative proteomics and tissue microarray profiling indicate the association between overexpressed serum proteins and non-small cell lung cancer. PloS one 7(12), e51748 (2012).
  • Edwards AM, Isserlin R, Bader GD, Frye SV, Willson TM, Yu FH. Too many roads not taken. Nature 470(7333), 163–165 (2011).
  • Whiteaker JR, Lin C, Kennedy J et al. A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat. Biotechnol. 29(7), 625–634 (2011).
  • Addona TA, Shi X, Keshishian H et al. A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease. Nat. Biotechnol. 29(7), 635–643 (2011).
  • Latterich M, Schnitzer JE. Streamlining biomarker discovery. Nat. Biotechnol. 29(7), 600–602 (2011).
  • Geiger T, Cox J, Ostasiewicz P, Wisniewski JR, Mann M. Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat. Methods 7(5), 383–385 (2010).
  • Li J, Su Z, Ma ZQ et al. A bioinformatics workflow for variant peptide detection in shotgun proteomics. Mol. Cell. Proteomics 10(5), M110 006536 (2011).
  • Sheynkman GM, Shortreed MR, Frey BL, Smith LM. Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq. Mol. Cell. Proteomics 12(8), 2341–2353 (2013).
  • Ostasiewicz P, Zielinska DF, Mann M, Wisniewski JR. Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry. J. Proteome Res. 9(7), 3688–3700 (2010).
  • Pham TV, Piersma SR, Oudgenoeg G, Jimenez CR. Label-free mass spectrometry-based proteomics for biomarker discovery and validation. Expert Rev. Molecular Diagn. 12(4), 343–359 (2012).
  • Ong SE, Blagoev B, Kratchmarova 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).
  • Ross PL, Huang YN, Marchese JN et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3(12), 1154–1169 (2004).
  • Plumb RS, Johnson KA, Rainville P et al. UPLC/MS(E); a new approach for generating molecular fragment information for biomarker structure elucidation. Rapid Commun. Mass Spectrom. 20(13), 1989–1994 (2006).

Websites