Development of a targeted selected ion monitoring assay for the elucidation of protease induced structural changes in cardiac troponin T

Journal of Proteomics

Volumn 136, Issue , 2016, Pages 123-132

  Streng, Alexander S ^a   de Boer, Douwe ^a   Bouwman, Freek G ^b   Mariman, Edwin C M ^b   Scholten, Arjen ^c,d,e   Van Dieijen Visser, Marja P ^a   Wodzig, Will K W H ^a  

^a MAASTRICHT UNIVERSITY MEDICAL CENTER   (Netherlands)

^b MAASTRICHT UNIVERSITY   (Netherlands)

^c UTRECHT UNIVERSITY   (Netherlands)

^d UTRECHT UNIVERSITY   (Netherlands)

^e JOHNSON AND JOHNSON   (United States)

Author keywords

Cardiac troponin T; Relative quantification; Selected ion monitoring; Targeted proteomics

Indexed keywords

BIOLOGICAL MARKER; PROTEINASE; TROPONIN T; PEPTIDE HYDROLASE;

ACUTE HEART INFARCTION; AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; FRACTIONATION; HUMAN; IMMUNOPRECIPITATION; ION MONITORING; MASS SPECTROMETER; MASS SPECTROMETRY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CLEAVAGE; PROTEIN DEGRADATION; PROTEIN ISOLATION; PROTEIN STRUCTURE; QUALITY CONTROL; TANDEM MASS SPECTROMETRY; ULTRA PERFORMANCE LIQUID CHROMATOGRAPHY; BLOOD; CHEMISTRY; HEART INFARCTION; METABOLISM;

HUMANS; MASS SPECTROMETRY; MYOCARDIAL INFARCTION; PEPTIDE HYDROLASES; PROTEOLYSIS; TROPONIN T;

EID: 84959300958     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2015.12.028     Document Type: Article

References (48)

1. Katrukha I.A. Human cardiac troponin complex. Structure and functions. Biochemistry (Mosc) 2013, 78:1447-1465.
2. Streng A.S., de Boer D., van der Velden J., van Dieijen-Visser M.P., Wodzig W.K. Posttranslational modifications of cardiac troponin T: an overview. J. Mol. Cell. Cardiol. 2013, 63:47-56.
3. Wei B., Jin J.P. Troponin T isoforms and posttranscriptional modifications: evolution, regulation and function. Arch. Biochem. Biophys. 2011, 505:144-154.
4. Thygesen K., Alpert J.S., Jaffe A.S., Simoons M.L., Chaitman B.R., White H.D., Joint ESCAAHAWHFTFfUDoMI, Authors/Task Force Members C, Thygesen K., Alpert J.S., White H.D., Biomarker S, Jaffe A.S., Katus H.A., Apple F.S., Lindahl B., Morrow D.A., Subcommittee ECG, Chaitman B.R., Clemmensen P.M., Johanson P., Hod H., Imaging S., Underwood R., Bax J.J., Bonow J.J., Pinto F., Gibbons R.J., Classification S, Fox K.A., Atar D., Newby L.K., Galvani M., Hamm C.W., Intervention S, Uretsky B.F., Steg P.G., Wijns W., Bassand J.P., Menasche P., Ravkilde J., Trials, Registries S, Ohman E.M., Antman E.M., Wallentin L.C., Armstrong P.W., Simoons M.L., Trials, Registries S, Januzzi J.L., Nieminen M.S., Gheorghiade M., Filippatos G., Trials, Registries S, Luepker R.V., Fortmann S.P., Rosamond W.D., Levy D., Wood D., Trials, Registries S, Smith S.C., Hu D., Lopez-Sendon J.L., Robertson R.M., Weaver D., Tendera M., Bove A.A., Parkhomenko A.N., Vasilieva E.J., Mendis S., Guidelines ESCCfP, Bax J.J., Baumgartner H., Ceconi C., Dean V., Deaton C., Fagard R., Funck-Brentano C., Hasdai D., Hoes A., Kirchhof P., Knuuti J., Kolh P., McDonagh T., Moulin C., Popescu B.A., Reiner Z., Sechtem U., Sirnes P.A., Tendera M., Torbicki A., Vahanian A., Windecker S., Document R, Morais J., Aguiar C., Almahmeed W., Arnar D.O., Barili F., Bloch K.D., Bolger A.F., Botker H.E., Bozkurt B., Bugiardini R., Cannon C., de Lemos J., Eberli F.R., Escobar E., Hlatky M., James S., Kern K.B., Moliterno D.J., Mueller C., Neskovic A.N., Pieske B.M., Schulman S.P., Storey R.F., Taubert K.A., Vranckx P., Wagner D.R. Third universal definition of myocardial infarction. J. Am. Coll. Cardiol. 2012, 60:1581-1598.
5. de Lemos J.A. Increasingly sensitive assays for cardiac troponins: a review. J. Am. Med. Assoc. 2013, 309:2262-2269.
6. Mingels A.M., Cobbaert C.M., de Jong N., van den Hof W.F., van Dieijen-Visser M.P. Time- and temperature-dependent stability of troponin standard reference material 2921 in serum and plasma. Clin. Chem. Lab. Med. 2012, 50:1681-1684.
7. Michielsen E.C., Diris J.H., Kleijnen V.W., Wodzig W.K., Van Dieijen-Visser M.P. Investigation of release and degradation of cardiac troponin T in patients with acute myocardial infarction. Clin. Biochem. 2007, 40:851-855.
8. Cardinaels E.P., Mingels A.M., van Rooij T., Collinson P.O., Prinzen F.W., van Dieijen-Visser M.P. Time-dependent degradation pattern of cardiac troponin T following myocardial infarction. Clin. Chem. 2013, 59:1083-1090.
9. Bates K.J., Hall E.M., Fahie-Wilson M.N., Kindler H., Bailey C., Lythall D., Lamb E.J. Circulating immunoreactive cardiac troponin forms determined by gel filtration chromatography after acute myocardial infarction. Clin. Chem. 2010, 56:952-958.
10. Biener M., Katus H.A., Giannitsis E. Challenges of serial troponin testing: a symphony in need for harmony. Int. J. Cardiol. 2013, 168:4542.
11. Aebersold R., Mann M. Mass spectrometry-based proteomics. Nature 2003, 422:198-207.
12. Domon B., Aebersold R. Mass spectrometry and protein analysis. Science 2006, 312:212-217.
13. Bell A.W., Deutsch E.W., Au C.E., Kearney R.E., Beavis R., Sechi S., Nilsson T., Bergeron J.J., Group H.T.S.W. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat. Methods 2009, 6:423-430.
14. Aebersold R. A stress test for mass spectrometry-based proteomics. Nat. Methods 2009, 6:411-412.
15. Shi T., Sun X., Gao Y., Fillmore T.L., Schepmoes A.A., Zhao R., He J., Moore R.J., Kagan J., Rodland K.D., Liu T., Liu A.Y., Smith R.D., Tang K., Camp D.G., Qian W.J. Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion. J. Proteome Res. 2013, 12:3353-3361.
16. Domon B., Aebersold R. Options and considerations when selecting a quantitative proteomics strategy. Nat. Biotechnol. 2010, 28:710-721.
17. Gallien S., Duriez E., Crone C., Kellmann M., Moehring T., Domon B. Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer. Mol. Cell. Proteomics 2012, 11:1709-1723.
18. Lange V., Picotti P., Domon B., Aebersold R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol. Syst. Biol. 2008, 4:222.
19. Gallien S., Duriez E., Domon B. Selected reaction monitoring applied to proteomics. J. Mass Spectrom. 2011, 46:298-312.
20. Picotti P., Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat. Methods 2012, 9:555-566.
21. Peterson A.C., Russell J.D., Bailey D.J., Westphall M.S., Coon J.J. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol. Cell. Proteomics 2012, 11:1475-1488.
22. Lesur A., Domon B. Advances in high-resolution accurate mass spectrometry application to targeted proteomics. Proteomics 2015, 15:880-890.
23. Kuster B., Schirle M., Mallick P., Aebersold R. Scoring proteomes with proteotypic peptide probes. Nat. Rev. Mol. Cell Biol. 2005, 6:577-583.
24. Holman S.W., Sims P.F., Eyers C.E. The use of selected reaction monitoring in quantitative proteomics. Bioanalysis 2012, 4:1763-1786.
25. Villanueva J., Carrascal M., Abian J. Isotope dilution mass spectrometry for absolute quantification in proteomics: concepts and strategies. J. Proteomics 2014, 96:184-199.
26. Carr S.A., Abbatiello S.E., Ackermann B.L., Borchers C., Domon B., Deutsch E.W., Grant R.P., Hoofnagle A.N., Huttenhain R., Koomen J.M., Liebler D.C., Liu T., MacLean B., Mani D.R., Mansfield E., Neubert H., Paulovich A.G., Reiter L., Vitek O., Aebersold R., Anderson L., Bethem R., Blonder J., Boja E., Botelho J., Boyne M., Bradshaw R.A., Burlingame A.L., Chan D., Keshishian H., Kuhn E., Kinsinger C., Lee J.S., Lee S.W., Moritz R., Oses-Prieto J., Rifai N., Ritchie J., Rodriguez H., Srinivas P.R., Townsend R.R., Van Eyk J., Whiteley G., Wiita A., Weintraub S. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol. Cell. Proteomics 2014, 13:907-917.
27. Michielsen E.C., Diris J.H., Hackeng C.M., Wodzig W.K., Van Dieijen-Visser M.P. Highly sensitive immunoprecipitation method for extracting and concentrating low-abundance proteins from human serum. Clin. Chem. 2005, 51:222-224.
28. Saveliev S.V., Woodroofe C.C., Sabat G., Adams C.M., Klaubert D., Wood K., Urh M. Mass spectrometry compatible surfactant for optimized in-gel protein digestion. Anal. Chem. 2013, 85:907-914.
29. MacLean B., Tomazela D.M., Shulman N., Chambers M., Finney G.L., Frewen B., Kern R., Tabb D.L., Liebler D.C., MacCoss M.J. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 2010, 26:966-968.
30. Streng A.S., De Boer D., Bouwman F., Mariman E.C., Scholten A., Van Dieijen-Visser M.P., Wodzig W.K. Validation, optimisation, and application data in support of the development of a targeted selected ion monitoring assay for degraded cardiac troponin T Data in brief 2016, submitted.
31. Tsiatsiani L., Heck A.J. Proteomics beyond trypsin. FEBS J. 2015, 282:2612-2626.
32. Wu C.H., Yeh L.S., Huang H., Arminski L., Castro-Alvear J., Chen Y., Hu Z., Kourtesis P., Ledley R.S., Suzek B.E., Vinayaka C.R., Zhang J., Barker W.C. The protein information resource. Nucleic Acids Res. 2003, 31:345-347.
33. Chen C., Li Z., Huang H., Suzek B.E., Wu C.H., UniProt C A fast Peptide Match service for UniProt Knowledgebase. Bioinformatics 2013, 29:2808-2809.
34. Hughes N.C., Wong E.Y., Fan J., Bajaj N. Determination of carryover and contamination for mass spectrometry-based chromatographic assays. AAPS J. 2007, 9:E353-E360.
35. Jarolim P. High sensitivity cardiac troponin assays in the clinical laboratories. Clin. Chem. Lab. Med. 2015, 53:635-652.
36. Zhang Z., Biesiadecki B.J., Jin J.P. Selective deletion of the NH2-terminal variable region of cardiac troponin T in ischemia reperfusion by myofibril-associated mu-calpain cleavage. Biochemistry 2006, 45:11681-11694.
37. Streng A.S., Jacobs L.H.J., Schwenk R.W., Cardinaels E.P.M., Meex S.J.R., Glatz J.F.C., Wodzig W.K.W.H., van Dieijen-Visser M.P. Cardiac troponin in ischemic cardiomyocytes: intracellular decrease before onset of cell death. Exp. Mol. Pathol. 2014, 96:339-345.
38. Mamidi R., Mallampalli S.L., Wieczorek D.F., Chandra M. Identification of two new regions in the N-terminus of cardiac troponin T that have divergent effects on cardiac contractile function. J. Physiol. 2013, 591:1217-1234.
39. Bizzarri M., Cavaliere C., Foglia P., Guarino C., Samperi R., Lagana A. A label-free method based on MALDI-TOF mass spectrometry for the absolute quantitation of troponin T in mouse cardiac tissue. Anal. Bioanal. Chem. 2008, 391:1969-1976.
40. Cavaliere C., Cucci F., Guarino C., Gubbiotti R., Samperi R., Lagana A. Absolute quantification of cardiac troponin T by means of liquid chromatography/triple quadrupole tandem mass spectrometry. Rapid Commun. Mass Spectrom. 2008, 22:1159-1167.
41. Keshishian H., Addona T., Burgess M., Mani D.R., Shi X., Kuhn E., Sabatine M.S., Gerszten R.E., Carr S.A. Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics 2009, 8:2339-2349.
42. Lowenthal M.S., Gasca-Aragon H., Schiel J.E., Dodder N.G., Bunk D.M. A quantitative LC-MS/MS method for comparative analysis of capture-antibody affinity toward protein antigens. J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 2011, 879:2726-2732.
43. Olkowicz M., Rybakowska I., Chlopicki S., Smolenski R.T. Development and analytical comparison of microflow and nanoflow liquid chromatography/mass spectrometry procedures for quantification of cardiac troponin T in mouse hearts. Talanta 2015, 131:510-520.
44. Communal C., Sumandea M., de Tombe P., Narula J., Solaro R.J., Hajjar R.J. Functional consequences of caspase activation in cardiac myocytes. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:6252-6256.
45. Fahlman R.P., Chen W., Overall C.M. Absolute proteomic quantification of the activity state of proteases and proteolytic cleavages using proteolytic signature peptides and isobaric tags. J. Proteomics 2014, 100:79-91.
46. Kleifeld O., Doucet A., auf dem Keller U., Prudova A., Schilling O., Kainthan R.K., Starr A.E., Foster L.J., Kizhakkedathu J.N., Overall C.M. Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products. Nat. Biotechnol. 2010, 28:281-288.
47. Venne A.S., Vogtle F.N., Meisinger C., Sickmann A., Zahedi R.P. Novel highly sensitive, specific, and straightforward strategy for comprehensive N-terminal proteomics reveals unknown substrates of the mitochondrial peptidase Icp55. J. Proteome Res. 2013, 12:3823-3830.
48. Vizcaino J.A., Cote R.G., Csordas A., Dianes J.A., Fabregat A., Foster J.M., Griss J., Alpi E., Birim M., Contell J., O'Kelly G., Schoenegger A., Ovelleiro D., Perez-Riverol Y., Reisinger F., Rios D., Wang R., Hermjakob H. The Proteomics Identifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 2013, 41(D1):D1063-D1069.