Mass spectrometry for translational proteomics: progress and clinical implications
Tóm tắt
The utility of mass spectrometry (MS)-based proteomic analyses and their clinical applications have been increasingly recognized over the past decade due to their high sensitivity, specificity and throughput. MS-based proteomic measurements have been used in a wide range of biological and biomedical investigations, including analysis of cellular responses and disease-specific post-translational modifications. These studies greatly enhance our understanding of the complex and dynamic nature of the proteome in biology and disease. Some MS techniques, such as those for targeted analysis, are being successfully applied for biomarker verification, whereas others, including global quantitative analysis (for example, for biomarker discovery), are more challenging and require further development. However, recent technological improvements in sample processing, instrumental platforms, data acquisition approaches and informatics capabilities continue to advance MS-based applications. Improving the detection of significant changes in proteins through these advances shows great promise for the discovery of improved biomarker candidates that can be verified pre-clinically using targeted measurements, and ultimately used in clinical studies - for example, for early disease diagnosis or as targets for drug development and therapeutic intervention. Here, we review the current state of MS-based proteomics with regard to its advantages and current limitations, and we highlight its translational applications in studies of protein biomarkers.
Tài liệu tham khảo
Bendall SC, Simonds EF, Qiu P, Amir el-AD, Krutzik PO, Finck R, Bruggner RV, Melamed R, Trejo A, Ornatsky OI, Balderas RS, Plevritis SK, Sachs K, Pe'er D, Tanner SD, Nolan GP: Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science. 2011, 332: 687-696. 10.1126/science.1198704.
Addona TA, Shi X, Keshishian H, Mani DR, Burgess M, Gillette MA, Clauser KR, Shen D, Lewis GD, Farrell LA, Fifer MA, Sabatine MS, Gerszten RE, Carr SA: A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease. Nat Biotechnol. 2011, 29: 635-643. 10.1038/nbt.1899.
Whiteaker JR, Lin C, Kennedy J, Hou L, Trute M, Sokal I, Yan P, Schoenherr RM, Zhao L, Voytovich UJ, Kelly-Spratt KS, Krasnoselsky A, Gafken PR, Hogan JM, Jones LA, Wang P, Amon L, Chodosh LA, Nelson PS, McIntosh MW, Kemp CJ, Paulovich AG: A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat Biotechnol. 2011, 29: 625-634. 10.1038/nbt.1900.
Saffert RT, Cunningham SA, Ihde SM, Jobe KE, Mandrekar J, Patel R: Comparison of Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometer to BD Phoenix automated microbiology system for identification of gram-negative bacilli. J Clin Microbiol. 2011, 49: 887-892. 10.1128/JCM.01890-10.
Bizzini A, Durussel C, Bille J, Greub G, Prod'hom G: Performance of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of bacterial strains routinely isolated in a clinical microbiology laboratory. J Clin Microbiol. 2010, 48: 1549-1554. 10.1128/JCM.01794-09.
American Medical Association. Proteomics. [http://www.ama-assn.org/ama/pub/physician-resources/medical-science/genetics-molecular-medicine/current-topics/proteomics.page]
Pruitt K, Brown G, Tatusova T, Maglott D: The Reference Sequence (RefSeq) Database. The NCBI Handbook [Internet]. 9 October 2002 (updated 6 April 2012), [http://www.ncbi.nlm.nih.gov/books/NBK21091]
Pruitt KD, Tatusova T, Maglott DR: NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005, 33: D501-504. 10.1093/nar/gki476.
Chan IS, Ginsburg GS: Personalized medicine: progress and promise. Annu Rev Genomics Hum Genet. 2011, 12: 217-44. 10.1146/annurev-genom-082410-101446.
Hutchinson L: Personalized cancer medicine: era of promise and progress. Nat Rev Clin Oncol. 2011, 8: 121-10.1038/nrclinonc.2011.14.
Anderson NL, Anderson NG: The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics. 2002, 1: 845-867. 10.1074/mcp.R200007-MCP200.
Catalona WJ, Partin AW, Slawin KM, Brawer MK, Flanigan RC, Patel A, Richie JP, deKernion JB, Walsh PC, Scardino PT, Lange PH, Subong EN, Parson RE, Gasior GH, Loveland KG, Southwick PC: Use of the percentage of free prostate-specific antigen to enhance differentiation of prostate cancer from benign prostatic disease: a prospective multicenter clinical trial. JAMA. 1998, 279: 1542-1547. 10.1001/jama.279.19.1542.
Antman EM, Tanasijevic MJ, Thompson B, Schactman M, McCabe CH, Cannon CP, Fischer GA, Fung AY, Thompson C, Wybenga D, Braunwald E: Cardiac-specific troponin I levels to predict the risk of mortality in patients with acute coronary syndromes. N Engl J Med. 1996, 335: 1342-1349. 10.1056/NEJM199610313351802.
Danesh J, Wheeler JG, Hirschfield GM, Eda S, Eiriksdottir G, Rumley A, Lowe GD, Pepys MB, Gudnason V: C-reactive protein and other circulating markers of inflammation in the prediction of coronary heart disease. N Engl J Med. 2004, 350: 1387-1397. 10.1056/NEJMoa032804.
Gillette MA, Carr SA: Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat Biotechnol. 2006, 24: 971-983. 10.1038/nbt1235.
Anderson NL: The roles of multiple proteomic platforms in a pipeline for new diagnostics. Mol Cell Proteomics. 2005, 4: 1441-1444. 10.1074/mcp.I500001-MCP200.
Jacobs JM, Adkins JN, Qian WJ, Liu T, Shen Y, Camp DG, Smith RD: Utilizing human blood plasma for proteomic biomarker discovery. J Proteome Res. 2005, 4: 1073-1085. 10.1021/pr0500657.
Ricós C, Iglesias N, García-Lario JV, Simón M, Cava F, Hernández A, Perich C, Minchinela J, Alvarez V, Doménech MV, Jiménez CV, Biosca C, Tena R: Within-subject biological variation in disease: collated data and clinical consequences. Ann Clin Biochem. 2007, 44: 343-352. 10.1258/000456307780945633.
Nedelkov D, Kiernan UA, Niederkofler EE, Tubbs KA, Nelson RW: Population proteomics: the concept, attributes, and potential for cancer biomarker research. Mol Cell Proteomics. 2006, 5: 1811-1818. 10.1074/mcp.R600006-MCP200.
Mirsky P, Chatterjee A, Sauer-Budge AF, Sharon A: An automated, parallel processing approach to biomolecular sample preparation. J Lab Autom. 2012, 17: 116-124.
Unwin RD, Griffiths JR, Whetton AD: Simultaneous analysis of relative protein expression levels across multiple samples using iTRAQ isobaric tags with 2D nano LC-MS/MS. Nat Protoc. 2010, 5: 1574-1582. 10.1038/nprot.2010.123.
Gilar M, Greibrokk T: 2D LC - embraced by life-science research and drug development. J Sep Sci. 2012, 35: NA
Belov ME, Prasad S, Prior DC, Danielson WF, Weitz K, Ibrahim YM, Smith RD: Pulsed multiple reaction monitoring approach to enhancing sensitivity of a tandem quadrupole mass spectrometer. Anal Chem. 2011, 83: 2162-2171. 10.1021/ac103006b.
Ibrahim Y, Belov ME, Tolmachev AV, Prior DC, Smith RD: Ion funnel trap interface for orthogonal time-of-flight mass spectrometry. Anal Chem. 2007, 79: 7845-7852. 10.1021/ac071091m.
Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R: 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. 2012, 11: O111.016717-10.1074/mcp.O111.016717.
Panchaud A, Scherl A, Shaffer SA, von Haller PD, Kulasekara HD, Miller SI, Goodlett DR: Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Anal Chem. 2009, 81: 6481-6488. 10.1021/ac900888s.
Röst H, Malmström L, Aebersold R: A computational tool to detect and avoid redundancy in selected reaction monitoring. Mol Cell Proteomics. 2012, 11: 540-549. 10.1074/mcp.M111.013045.
Schilling B, Rardin MJ, MacLean BX, Zawadzka AM, Frewen BE, Cusack MP, Sorensen DJ, Bereman MS, Jing E, Wu CC, Verdin E, Kahn CR, Maccoss MJ, Gibson BW: Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation. Mol Cell Proteomics. 2012, 11: 202-214. 10.1074/mcp.M112.017707.
Farrah T, Deutsch EW, Kreisberg R, Sun Z, Campbell DS, Mendoza L, Kusebauch U, Brusniak MY, Hüttenhain R, Schiess R, Selevsek N, Aebersold R, Moritz RL: PASSEL: The PeptideAtlas SRMexperiment library. Proteomics. 2012, 12: 1170-1175. 10.1002/pmic.201100515.
McAlister GC, Coon JJ: Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat Methods. 2008, 5: 959-964. 10.1038/nmeth.1260.
Washburn MP, Wolters D, Yates JR: Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol. 2001, 19: 242-247. 10.1038/85686.
Schuchard M, Melm C, Crawford H, Chapman S, Cockrill S, Ray K, Mehigh R, Chen D, Scott G: Specific depletion of twenty high abundance proteins from human plasma. Poster presented at NCI Proteomic Technologies Reagents Resource Workshop, 12-13. 2005, [http://www.scribd.com/doc/12287730/Specific-Depletion-of-Twenty-High-Abundance-Proteins]December
Shi T, Zhou JY, Gritsenko MA, Hossain M, Camp DG, Smith RD, Qian WJ: IgY14 and SuperMix immunoaffinity separations coupled with liquid chromatography-mass spectrometry for human plasma proteomics biomarker discovery. Methods. 2012, 56: 246-253. 10.1016/j.ymeth.2011.09.001.
Qian WJ, Kaleta DT, Petritis BO, Jiang H, Liu T, Zhang X, Mottaz HM, Varnum SM, Camp DG, Huang L, Fang X, Zhang WW, Smith RD: Enhanced detection of low abundance human plasma proteins using a tandem IgY12-SuperMix immunoaffinity separation strategy. Mol Cell Proteomics. 2008, 7: 1963-1973. 10.1074/mcp.M800008-MCP200.
Zhou JY, Petritis BO, Petritis K, Norbeck AD, Weitz KK, Moore RJ, Camp DG, Kulkarni RN, Smith RD, Qian WJ: Mouse-specific tandem IgY7-SuperMix immunoaffinity separations for improved LC-MS/MS coverage of the plasma proteome. J Proteome Res. 2009, 8: 5387-5395. 10.1021/pr900564f.
Faca V, Pitteri SJ, Newcomb L, Glukhova V, Phanstiel D, Krasnoselsky A, Zhang Q, Struthers J, Wang H, Eng J, Fitzgibbon M, McIntosh M, Hanash S: Contribution of protein fractionation to depth of analysis of the serum and plasma proteomes. J Proteome Res. 2007, 6: 3558-3565. 10.1021/pr070233q.
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. 2002, 74: 4235-4249. 10.1021/ac0202280.
Dowell JA, Frost DC, Zhang J, Li L: Comparison of two-dimensional fractionation techniques for shotgun proteomics. Anal Chem. 2008, 80: 6715-6723. 10.1021/ac8007994.
Perkins DN, Pappin DJ, Creasy DM, Cottrell JS: Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis. 1999, 20: 3551-3567. 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2.
Yates JR, Eng JK, McCormack AL, Schieltz D: Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal Chem. 1995, 67: 1426-1436. 10.1021/ac00104a020.
Beavis RC, Fenyo D: A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal Chem. 2003, 75: 768-774. 10.1021/ac0258709.
Nesvizhskii AI: A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics. 2010, 73: 2092-2123. 10.1016/j.jprot.2010.08.009.
Gupta N, Bandeira N, Keich U, Pevzner PA: Target-decoy approach and false discovery rate: when things may go wrong. J Am Soc Mass Spectrom. 2011, 22: 1111-1120. 10.1007/s13361-011-0139-3.
Kim S, Gupta N, Pevzner PA: Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J Proteome Res. 2008, 7: 3354-3363. 10.1021/pr8001244.
Xie F, Liu T, Qian WJ, Petyuk VA, Smith RD: Liquid chromatography-mass spectrometry-based quantitative proteomics. J Biol Chem. 2011, 286: 25443-25449. 10.1074/jbc.R110.199703.
Goshe MB, Smith RD: Stable isotope-coded proteomic mass spectrometry. Curr Opin Biotechnol. 2003, 14: 101-109. 10.1016/S0958-1669(02)00014-9.
Geiger T, Cox J, Ostasiewicz P, Wisniewski JR, Mann M: Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat Methods. 2010, 7: 383-385. 10.1038/nmeth.1446.
Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ: Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics. 2004, 3: 1154-1169. 10.1074/mcp.M400129-MCP200.
Zieske LR: A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies. J Exp Bot. 2006, 57: 1501-1508. 10.1093/jxb/erj168.
Qian WJ, Liu T, Petyuk VA, Gritsenko MA, Petritis BO, Polpitiya AD, Kaushal A, Xiao W, Finnerty CC, Jeschke MG, Jaitly N, Monroe ME, Moore RJ, Moldawer LL, Davis RW, Tompkins RG, Herndon DN, Camp DG, Smith RD, Inflammation and the Host Response to Injury Large Scale Collaborative Research Program: Large-scale multiplexed quantitative discovery proteomics enabled by the use of an (18)O-labeled "universal" reference sample. J Proteome Res. 2009, 8: 290-299. 10.1021/pr800467r.
Nielsen ML, Vermeulen M, Bonaldi T, Cox J, Moroder L, Mann M: Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry. Nat Methods. 2008, 5: 459-460. 10.1038/nmeth0608-459.
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. 2006, 25: 450-482. 10.1002/mas.20071.
Scicchitano MS, Dalmas DA, Boyce RW, Thomas HC, Frazier KS: Protein extraction of formalin-fixed, paraffin-embedded tissue enables robust proteomic profiles by mass spectrometry. J Histochem Cytochem. 2009, 57: 849-860. 10.1369/jhc.2009.953497.
Waldemarson S, Krogh M, Alaiya A, Kirik U, Schedvins K, Auer G, Hansson KM, Ossola R, Aebersold R, Lee H, Malmström J, James P: Protein expression changes in ovarian cancer during the transition from benign to malignant. J Proteome Res. 2012, 11: 2876-2889. 10.1021/pr201258q.
Angel TE, Jacobs JM, Spudich SS, Gritsenko MA, Fuchs D, Liegler T, Zetterberg H, Camp DG, Price RW, Smith RD: The cerebrospinal fluid proteome in HIV infection: change associated with disease severity. Clin Proteomics. 2012, 9: 3-10.1186/1559-0275-9-3.
Gallien S, Duriez E, Domon B: Selected reaction monitoring applied to proteomics. J Mass Spectrom. 2011, 46: 298-312. 10.1002/jms.1895.
Stahl-Zeng J, Lange V, Ossola R, Eckhardt K, Krek W, Aebersold R, Domon B: High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomics. 2007, 6: 1809-1817. 10.1074/mcp.M700132-MCP200.
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. 2004, 3: 235-244. 10.1021/pr034086h.
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. 2010, 9: 184-196. 10.1074/mcp.M900254-MCP200.
Hossain M, Kaleta DT, Robinson EW, Liu T, Zhao R, Page JS, Kelly RT, Moore RJ, Tang K, Camp DG, Qian WJ, Smith RD: Enhanced sensitivity for selected reaction monitoring mass spectrometry-based targeted proteomics using a dual stage electrodynamic ion funnel interface. Mol Cell Proteomics. 2011, 10: M000062-MCP201.
Picotti P, Lam H, Campbell D, Deutsch EW, Mirzaei H, Ranish J, Domon B, Aebersold R: A database of mass spectrometric assays for the yeast proteome. Nat Methods. 2008, 5: 913-914. 10.1038/nmeth1108-913.
SRM Atlas. [http://www.srmatlas.org/]
Lange V, Picotti P, Domon B, Aebersold R: Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol. 2008, 4: 222-
Beavis RC, Craig R, Cortens JP: Open source system for analyzing, validating, and storing protein identification data. J Proteome Res. 2004, 3: 1234-1242. 10.1021/pr049882h.
Fusaro VA, Mani DR, Mesirov JP, Carr SA: Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat Biotechnol. 2009, 27: 190-198. 10.1038/nbt.1524.
Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, Spiegelman CH, Zimmerman LJ, Ham AJ, Keshishian H, Hall SC, Allen S, Blackman RK, Borchers CH, Buck C, Cardasis HL, Cusack MP, Dodder NG, Gibson BW, Held JM, Hiltke T, Jackson A, Johansen EB, Kinsinger CR, Li J, Mesri M, Neubert TA, Niles RK, Pulsipher TC, Ransohoff D, et al: Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol. 2009, 27: 633-641. 10.1038/nbt.1546.
Suhr H: Plasma Chromatography. 1984, New York: Plenum Press
Mason E, McDaniel E: Transport Properites of Ions in Gases. 1988, New York: Wiley
Guevremont R, Siu KW, Wang J, Ding L: Combined ion mobility/time-of-flight mass spectrometry study of electrospray-generated ions. Anal Chem. 1997, 69: 3959-3965. 10.1021/ac970359e.
Baker ES, Tang K, Danielson WF, Prior DC, Smith RD: Simultaneous fragmentation of multiple ions using IMS drift time dependent collision energies. J Am Soc Mass Spectrom. 2008, 19: 411-419. 10.1016/j.jasms.2007.11.018.
Merenbloom SI, Koeniger SL, Valentine SJ, Plasencia MD, Clemmer DE: IMS-IMS and IMS-IMS-IMS/MS for separating peptide and protein fragment ions. Anal Chem. 2006, 78: 2802-2809. 10.1021/ac052208e.
Pringle SD, Giles K, Wildgoose JL, Williams JP, Slade SE, Thalassinos K, Bateman RH, Bowers MT, Scrivens JH: An investigation of the mobility separation of some peptide and protein ions using a new hybrid quadrupole/travelling wave IMS/oa-ToF instrument. Int J Mass Spectrom. 2007, 261: 1-12. 10.1016/j.ijms.2006.07.021.
Baker ES, Livesay EA, Orton DJ, Moore RJ, Danielson WF, Prior DC, Ibrahim YM, LaMarche BL, Mayampurath AM, Schepmoes AA, Hopkins DF, Tang K, Smith RD, Belov ME: An LC-IMS-MS platform providing increased dynamic range for high-throughput proteomic studies. J Proteome Res. 2010, 9: 997-1006. 10.1021/pr900888b.
Tang K, Shvartsburg AA, Lee HN, Prior DC, Buschbach MA, Li F, Tolmachev AV, Anderson GA, Smith RD: High-sensitivity ion mobility spectrometry/mass spectrometry using electrodynamic ion funnel interfaces. Anal Chem. 2005, 77: 3330-3339. 10.1021/ac048315a.
Shaffer SA, Tang K, Anderson GA, Prior DC, Udseth HR, Smith RD: A novel ion funnel for focusing ions at elevated pressure using electrospray ionization mass spectrometry. Rapid Commun Mass Spectrom. 1997, 11: 1813-1817. 10.1002/(SICI)1097-0231(19971030)11:16<1813::AID-RCM87>3.0.CO;2-D.
Lindner M, Hoffmann GF, Matern D: Newborn screening for disorders of fatty-acid oxidation: experience and recommendations from an expert meeting. J Inherit Metab Dis. 2010, 33: 521-526. 10.1007/s10545-010-9076-8.
Smith RD: Mass spectrometry in biomarker applications: from untargeted discovery to targeted verification, and implications for platform convergence and clinical application. Clin Chem. 2012, 58: 528-530. 10.1373/clinchem.2011.180596.
Surinova S, Schiess R, Hüttenhain R, Cerciello F, Wollscheid B, Aebersold R: On the development of plasma protein biomarkers. J Proteome Res. 2011, 10: 5-16. 10.1021/pr1008515.