دورية أكاديمية

Mass Spectrometry-Based Proteomics for Biomarker Discovery.

التفاصيل البيبلوغرافية
العنوان: Mass Spectrometry-Based Proteomics for Biomarker Discovery.
المؤلفون: Cao Z; Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA., Yu LR; Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA. Lirong.yu@fda.hhs.gov.
المصدر: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2022; Vol. 2486, pp. 3-17.
نوع المنشور: Journal Article; Research Support, U.S. Gov't, P.H.S.
اللغة: English
بيانات الدورية: Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE
أسماء مطبوعة: Publication: Totowa, NJ : Humana Press
Original Publication: Clifton, N.J. : Humana Press,
مواضيع طبية MeSH: Proteomics*/methods , Tandem Mass Spectrometry*/methods, Biomarkers ; Chromatography, Liquid/methods ; Proteome/analysis
مستخلص: Proteomics plays a pivotal role in systems medicine, in which pharmacoproteomics and toxicoproteomics have been developed to address questions related to efficacy and toxicity of drugs. Mass spectrometry is the core technology for quantitative proteomics, providing the capabilities of identification and quantitation of thousands of proteins. The technology has been applied to biomarker discovery and understanding the mechanisms of drug action. Both stable isotope labeling of proteins or peptides and label-free approaches have been incorporated with multidimensional LC separation and tandem mass spectrometry (LC-MS/MS) to increase the coverage and depth of proteome analysis. A protocol of such an approach exemplified by dimethyl labeling in combination with 2D-LC-MS/MS is described. With further development of novel proteomic tools and increase in sample throughput, the full spectrum of mass spectrometry-based proteomic research will greatly advance systems medicine.
(© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
References: Wasinger VC, Cordwell SJ, Cerpa-Poljak A et al (1995) Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis 16(7):1090–1094. (PMID: 10.1002/elps.11501601185)
Humphery-Smith I, Cordwell SJ, Blackstock WP (1997) Proteome research: complementarity and limitations with respect to the RNA and DNA worlds. Electrophoresis 18(8):1217–1242. https://doi.org/10.1002/elps.1150180804. (PMID: 10.1002/elps.1150180804)
Wetmore BA, Merrick BA (2004) Toxicoproteomics: proteomics applied to toxicology and pathology. Toxicol Pathol 32(6):619–642. (PMID: 10.1080/01926230490518244)
Monsinjon T, Knigge T (2007) Proteomic applications in ecotoxicology. Proteomics 7(16):2997–3009. https://doi.org/10.1002/pmic.200700101. (PMID: 10.1002/pmic.200700101)
Yu LR (2011) Pharmacoproteomics and toxicoproteomics: the field of dreams. J Proteome 74(12):2549–2553. https://doi.org/10.1016/j.jprot.2011.10.001 . S1874-3919(11)00487-8 [pii]. (PMID: 10.1016/j.jprot.2011.10.001)
O’Farrell PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250(10):4007–4021. (PMID: 10.1016/S0021-9258(19)41496-8)
Tanaka K, Waki H, Ido Y et al (1988) Protein and polymer analyses up to m/z 100 000 by laser ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 2(8):151–153. (PMID: 10.1002/rcm.1290020802)
Karas M, Hillenkamp F (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 60(20):2299–2301. (PMID: 10.1021/ac00171a028)
Fenn JB, Mann M, Meng CK et al (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246(4926):64–71. (PMID: 10.1126/science.2675315)
Zhu H, Bilgin M, Bangham R et al (2001) Global analysis of protein activities using proteome chips. Science 293(5537):2101–2105. (PMID: 10.1126/science.1062191)
Gold L, Walker JJ, Wilcox SK et al (2012) Advances in human proteomics at high scale with the SOMAscan proteomics platform. New Biotechnol 29(5):543–549. https://doi.org/10.1016/j.nbt.2011.11.016 . S1871-6784(11)00265-2 [pii]. (PMID: 10.1016/j.nbt.2011.11.016)
Berggrund M, Enroth S, Lundberg M et al (2019) Identification of candidate plasma protein biomarkers for cervical cancer using the multiplex proximity extension assay. Mol Cell Proteomics 18(4):735–743. https://doi.org/10.1074/mcp.RA118.001208 . S1535-9476(20)31837-5 [pii], RA118.001208 [pii]. (PMID: 10.1074/mcp.RA118.001208)
Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422(6928):198–207. (PMID: 10.1038/nature01511)
Hanke S, Besir H, Oesterhelt D et al (2008) Absolute SILAC for accurate quantitation of proteins in complex mixtures down to the attomole level. J Proteome Res 7(3):1118–1130. https://doi.org/10.1021/pr7007175. (PMID: 10.1021/pr7007175)
Belov ME, Gorshkov MV, Udseth HR et al (2000) Zeptomole-sensitivity electrospray ionization—Fourier transform ion cyclotron resonance mass spectrometry of proteins. Anal Chem 72(10):2271–2279. (PMID: 10.1021/ac991360b)
Shen Y, Smith RD (2005) Advanced nanoscale separations and mass spectrometry for sensitive high-throughput proteomics. Expert Rev Proteomics 2(3):431–447. https://doi.org/10.1586/14789450.2.3.431. (PMID: 10.1586/14789450.2.3.431)
Olsen JV, de Godoy LM, Li G et al (2005) Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol Cell Proteomics 4(12):2010–2021. (PMID: 10.1074/mcp.T500030-MCP200)
Williams DK Jr, Muddiman DC (2007) Parts-per-billion mass measurement accuracy achieved through the combination of multiple linear regression and automatic gain control in a Fourier transform ion cyclotron resonance mass spectrometer. Anal Chem 79(13):5058–5063. https://doi.org/10.1021/ac0704210. (PMID: 10.1021/ac0704210)
Karas M, Bachmann D, Bahr U et al (1987) Matrix-assisted ultraviolet laser desorption of non-volatile compounds. Int J Mass Spectrom Ion Process 78:53. (PMID: 10.1016/0168-1176(87)87041-6)
Dole M, Mack LL, Hines RL et al (1968) Molecular beams of macroions. J Chem Phys 49(5):2240. (PMID: 10.1063/1.1670391)
Yu L-R, Gao Y, Mendrick DL (2011) Mass spectrometry-based proteomics in systems toxicology. In: Casciano DA, Sahu SC (eds) Handbook of Systems Toxicology. John Wiley and Sons, Ltd., p. 177–196. https://doi.org/10.1002/9780470744307.gat212.
Yu LR, Conrads TP, Veenstra TD (2005) Mass spectrometry instrumentation. In: Cazes J (ed) Ewing’s analytical instrumentation handbook. Marcel Dekker, Inc., New York, NY, pp. 429–443.
Yost RA, Boyd RK (1990) Tandem mass spectrometry: quadrupole and hybrid instruments. Methods Enzymol 193:154–200. (PMID: 10.1016/0076-6879(90)93415-H)
Stafford GC Jr, Kelley PE, Syka JEP et al (1984) Recent improvements in and analytical applications of advanced ion trap technology. Int J Mass Spectrom Ion Process 60(1):85–98. (PMID: 10.1016/0168-1176(84)80077-4)
Schwartz JC, Senko MW, Syka JE (2002) A two-dimensional quadrupole ion trap mass spectrometer. J Am Soc Mass Spectrom 13(6):659–669. (PMID: 10.1016/S1044-0305(02)00384-7)
Hager JW (2002) A new linear ion trap mass spectrometer. Rapid Commun Mass Spectrom 16(6):512–526. (PMID: 10.1002/rcm.607)
Douglas DJ, Frank AJ, Mao D (2005) Linear ion traps in mass spectrometry. Mass Spectrom Rev 24(1):1–29. https://doi.org/10.1002/mas.20004. (PMID: 10.1002/mas.20004)
Cotter RJ (1997) Time-of-flight mass spectrometry: instrumentation and applications in biological research. Americfan Chemical Society, Washington, DC, p 350.
Medzihradszky KF, Campbell JM, Baldwin MA et al (2000) The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer. Anal Chem 72(3):552–558. (PMID: 10.1021/ac990809y)
Suckau D, Resemann A, Schuerenberg M et al (2003) A novel MALDI LIFT-TOF/TOF mass spectrometer for proteomics. Anal Bioanal Chem 376(7):952–965. https://doi.org/10.1007/s00216-003-2057-0. (PMID: 10.1007/s00216-003-2057-0)
Chernushevich IV, Loboda AV, Thomson BA (2001) An introduction to quadrupole-time-of-flight mass spectrometry. J Mass Spectrom 36(8):849–865. https://doi.org/10.1002/jms.207. (PMID: 10.1002/jms.207)
Makarov A (2000) Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis. Anal Chem 72(6):1156–1162. (PMID: 10.1021/ac991131p)
Hardman M, Makarov AA (2003) Interfacing the orbitrap mass analyzer to an electrospray ion source. Anal Chem 75(7):1699–1705. (PMID: 10.1021/ac0258047)
Makarov A, Denisov E, Lange O (2009) Performance evaluation of a high-field Orbitrap mass analyzer. J Am Soc Mass Spectrom 20(8):1391–1396. https://doi.org/10.1016/j.jasms.2009.01.005 . S1044-0305(09)00011-7 [pii]. (PMID: 10.1016/j.jasms.2009.01.005)
Hu Q, Noll RJ, Li H et al (2005) The Orbitrap: a new mass spectrometer. J Mass Spectrom 40(4):430–443. https://doi.org/10.1002/jms.856. (PMID: 10.1002/jms.856)
Comisarow MB, Marshall AG (1974) Fourier transform ion cyclotron resonance spectroscopy. Chem Phys Lett 25(2):282–283. (PMID: 10.1016/0009-2614(74)89137-2)
Solouki T, Emmett MR, Guan S et al (1997) Detection, number, and sequence location of sulfur-containing amino acids and disulfide bridges in peptides by ultrahigh-resolution MALDI FTICR mass spectrometry. Anal Chem 69(6):1163–1168. (PMID: 10.1021/ac960885q)
Bruce JE, Anderson GA, Wen J et al (1999) High-mass-measurement accuracy and 100% sequence coverage of enzymatically digested bovine serum albumin from an ESI-FTICR mass spectrum. Anal Chem 71(14):2595–2599. (PMID: 10.1021/ac990231s)
Hakansson K, Emmett MR, Hendrickson CL et al (2001) High-sensitivity electron capture dissociation tandem FTICR mass spectrometry of microelectrosprayed peptides. Anal Chem 73(15):3605–3610. (PMID: 10.1021/ac010141z)
Schaffer LV, Millikin RJ, Miller RM et al (2019) Identification and quantification of proteoforms by mass spectrometry. Proteomics 19(10):e1800361. https://doi.org/10.1002/pmic.201800361. (PMID: 10.1002/pmic.201800361)
Zhang J, Guy MJ, Norman HS et al (2011) Top-down quantitative proteomics identified phosphorylation of cardiac troponin I as a candidate biomarker for chronic heart failure. J Proteome Res 10(9):4054–4065. https://doi.org/10.1021/pr200258m. (PMID: 10.1021/pr200258m)
Li W, Petruzziello F, Zhao N et al (2017) Separation and identification of mouse brain tissue microproteins using top-down method with high resolution nanocapillary liquid chromatography mass spectrometry. Proteomics 17(12). https://doi.org/10.1002/pmic.201600419.
Bouchal P, Dvorakova M, Scherl A et al (2013) Intact protein profiling in breast cancer biomarker discovery: protein identification issue and the solutions based on 3D protein separation, bottom-up and top-down mass spectrometry. Proteomics 13(7):1053–1058. https://doi.org/10.1002/pmic.201200121. (PMID: 10.1002/pmic.201200121)
Ntai I, Toby TK, LeDuc RD et al (2016) A method for label-free, differential top-down proteomics. Methods Mol Biol 1410:121–133. https://doi.org/10.1007/978-1-4939-3524-6_8. (PMID: 10.1007/978-1-4939-3524-6_8)
Calligaris D, Villard C, Lafitte D (2011) Advances in top-down proteomics for disease biomarker discovery. J Proteome 74(7):920–934. https://doi.org/10.1016/j.jprot.2011.03.030 . S1874-3919(11)00137-0 [pii]. (PMID: 10.1016/j.jprot.2011.03.030)
Gregorich ZR, Ge Y (2014) Top-down proteomics in health and disease: challenges and opportunities. Proteomics 14(10):1195–1210. https://doi.org/10.1002/pmic.201300432. (PMID: 10.1002/pmic.201300432)
Wiener MC, Sachs JR, Deyanova EG et al (2004) Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures. Anal Chem 76(20):6085–6096. (PMID: 10.1021/ac0493875)
Washburn MP, Wolters D, Yates JR 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19(3):242–247. (PMID: 10.1038/85686)
Ong SE, Mann M (2005) Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol 1(5):252–262. https://doi.org/10.1038/nchembio736 . nchembio736 [pii]. (PMID: 10.1038/nchembio736)
Wang M, You J, Bemis KG et al (2008) Label-free mass spectrometry-based protein quantification technologies in proteomic analysis. Brief Funct Genomic Proteomic 7(5):329–339. https://doi.org/10.1093/bfgp/eln031 . eln031 [pii]. (PMID: 10.1093/bfgp/eln031)
Pham TV, Piersma SR, Oudgenoeg G et al (2012) Label-free mass spectrometry-based proteomics for biomarker discovery and validation. Expert Rev Mol Diagn 12(4):343–359. https://doi.org/10.1586/erm.12.31. (PMID: 10.1586/erm.12.31)
Megger DA, Bracht T, Meyer HE et al (2013) Label-free quantification in clinical proteomics. Biochim Biophys Acta 1834(8):1581–1590. https://doi.org/10.1016/j.bbapap.2013.04.001 . S1570-9639(13)00155-6 [pii]. (PMID: 10.1016/j.bbapap.2013.04.001)
Conrads TP, Alving K, Veenstra TD et al (2001) Quantitative analysis of bacterial and mammalian proteomes using a combination of cysteine affinity tags and 15 N-metabolic labeling. Anal Chem 73(9):2132–2139.
Chen X, Smith LM, Bradbury EM (2000) Site-specific mass tagging with stable isotopes in proteins for accurate and efficient protein identification. Anal Chem 72(6):1134–1143.
Veenstra TD, Martinovic S, Anderson GA et al (2000) Proteome analysis using selective incorporation of isotopically labeled amino acids. J Am Soc Mass Spectrom 11(1):78–82.
Ong SE, Blagoev B, Kratchmarova I et al (2002) 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. (PMID: 10.1074/mcp.M200025-MCP200)
Kruger M, Moser M, Ussar S et al (2008) SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 134(2):353–364. https://doi.org/10.1016/j.cell.2008.05.033 . S0092-8674(08)00695-8 [pii]. (PMID: 10.1016/j.cell.2008.05.033)
Schnolzer M, Jedrzejewski P, Lehmann WD (1996) Protease-catalyzed incorporation of 18 O into peptide fragments and its application for protein sequencing by electrospray and matrix-assisted laser desorption/ionization mass spectrometry. Electrophoresis 17(5):945–953.
Yao X, Freas A, Ramirez J et al (2001) Proteolytic 18 O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal Chem 73(13):2836–2842.
Gygi SP, Rist B, Gerber SA et al (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17(10):994–999. https://doi.org/10.1038/13690. (PMID: 10.1038/13690)
Yu LR, Conrads TP, Uo T et al (2004) Evaluation of the acid-cleavable isotope-coded affinity tag reagents: application to camptothecin-treated cortical neurons. J Proteome Res 3(3):469–477. (PMID: 10.1021/pr034090t)
Ross PL, Huang YN, Marchese JN et al (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3(12):1154–1169. (PMID: 10.1074/mcp.M400129-MCP200)
Thompson A, Schafer J, Kuhn K et al (2003) Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 75(8):1895–1904. (PMID: 10.1021/ac0262560)
Hsu JL, Huang SY, Chow NH et al (2003) Stable-isotope dimethyl labeling for quantitative proteomics. Anal Chem 75(24):6843–6852. https://doi.org/10.1021/ac0348625. (PMID: 10.1021/ac0348625)
Hsu JL, Huang SY, Chen SH (2006) Dimethyl multiplexed labeling combined with microcolumn separation and MS analysis for time course study in proteomics. Electrophoresis 27(18):3652–3660. https://doi.org/10.1002/elps.200600147. (PMID: 10.1002/elps.200600147)
Gerber SA, Rush J, Stemman O et al (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A 100(12):6940–6945. (PMID: 10.1073/pnas.0832254100)
Beynon RJ, Doherty MK, Pratt JM et al (2005) Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat Methods 2(8):587–589. https://doi.org/10.1038/nmeth774 . nmeth774 [pii]. (PMID: 10.1038/nmeth774)
Brun V, Dupuis A, Adrait A et al (2007) Isotope-labeled protein standards: toward absolute quantitative proteomics. Mol Cell Proteomics 6(12):2139–2149. https://doi.org/10.1074/mcp.M700163-MCP200 . M700163-MCP200 [pii]. (PMID: 10.1074/mcp.M700163-MCP200)
Moulder R, Bhosale SD, Goodlett DR et al (2018) Analysis of the plasma proteome using iTRAQ and TMT-based Isobaric labeling. Mass Spectrom Rev 37(5):583–606. https://doi.org/10.1002/mas.21550. (PMID: 10.1002/mas.21550)
Wang H, Shi T, Qian WJ et al (2016) The clinical impact of recent advances in LC-MS for cancer biomarker discovery and verification. Expert Rev Proteomics 13(1):99–114. https://doi.org/10.1586/14789450.2016.1122529. (PMID: 10.1586/14789450.2016.1122529)
Li N, Zhan X (2020) Mass spectrometry-based mitochondrial proteomics in human ovarian cancers. Mass Spectrom Rev 39(5–6):471–498. https://doi.org/10.1002/mas.21618. (PMID: 10.1002/mas.21618)
Huang T, Armbruster MR, Coulton JB et al (2019) Chemical tagging in mass spectrometry for systems biology. Anal Chem 91(1):109–125. https://doi.org/10.1021/acs.analchem.8b04951. (PMID: 10.1021/acs.analchem.8b04951)
Wei J, Gao Y (2021) Early disease biomarkers can be found using animal models urine proteomics. Expert Rev Proteomics 18(5):363–378. https://doi.org/10.1080/14789450.2021.1937133. (PMID: 10.1080/14789450.2021.1937133)
Masuda T, Mori A, Ito S et al (2021) Quantitative and targeted proteomics-based identification and validation of drug efficacy biomarkers. Drug Metab Pharmacokinet 36:100361. https://doi.org/10.1016/j.dmpk.2020.09.006 . S1347-4367(20)30419-5 [pii]. (PMID: 10.1016/j.dmpk.2020.09.006)
Izquierdo I, García Á (2016) Platelet proteomics applied to the search for novel antiplatelet therapeutic targets. Expert Rev Proteomics 13(11):993–1006. https://doi.org/10.1080/14789450.2016.1246188. (PMID: 10.1080/14789450.2016.1246188)
Chambliss AB, Chan DW (2016) Precision medicine: from pharmacogenomics to pharmacoproteomics. Clin Proteomics 13:25. https://doi.org/10.1186/s12014-016-9127-8 . 9127 [pii]. (PMID: 10.1186/s12014-016-9127-8)
Boersema PJ, Raijmakers R, Lemeer S et al (2009) Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat Protoc 4(4):484–494. https://doi.org/10.1038/nprot.2009.21 . nprot.2009.21 [pii]. (PMID: 10.1038/nprot.2009.21)
Deng Z, Ye M, Bian Y et al (2014) Multiplex isotope dimethyl labeling of substrate peptides for high throughput kinase activity assay via quantitative MALDI MS. Chem Commun (Camb) 50(90):13960–13962. https://doi.org/10.1039/c4cc04906c. (PMID: 10.1039/c4cc04906c)
فهرسة مساهمة: Keywords: Biomarker; Liquid chromatography; Mass spectrometry; Protein quantitation; Proteomics; Stable isotope labeling; Tandem MS
المشرفين على المادة: 0 (Biomarkers)
0 (Proteome)
تواريخ الأحداث: Date Created: 20220419 Date Completed: 20220420 Latest Revision: 20220719
رمز التحديث: 20231215
DOI: 10.1007/978-1-0716-2265-0_1
PMID: 35437715
قاعدة البيانات: MEDLINE
الوصف
تدمد:1940-6029
DOI:10.1007/978-1-0716-2265-0_1