Multiple reaction monitoring enables precise quantification of 97 proteins in dried blood spots

Molecular and Cellular Proteomics

Volumn 14, Issue 11, 2015, Pages 3094-3104

  Chambers, Andrew G ^a   Percy, Andrew J ^a   Yang, Juncong ^a   Borchers, Christoph H ^a,b  

^a UNIVERSITY OF VICTORIA   (Canada)

^b UNIVERSITY OF VICTORIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

APOLIPOPROTEIN C2; APOLIPOPROTEIN D; CHOLINESTERASE; GALECTIN 3; INTERLEUKIN 6; NEUTROPHIL GELATINASE ASSOCIATED LIPOCALIN; PEPTIDE; PROTEIN; SERUM ALBUMIN; SOMATOMEDIN C; STABLE ISOTOPE; PLASMA PROTEIN;

ACCURACY; ARTICLE; CELL LYSATE; DRIED BLOOD SPOT TESTING; FREEZING; HEMATOCRIT; HUMAN; ISOTOPE LABELING; LIMIT OF DETECTION; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN DETERMINATION; STORAGE TEMPERATURE; BIOASSAY; DEVICES; ISOLATION AND PURIFICATION; LIQUID CHROMATOGRAPHY; PROCEDURES; PROTEIN STABILITY; PROTEOMICS; REPRODUCIBILITY; STANDARDS; TANDEM MASS SPECTROMETRY;

BIOLOGICAL ASSAY; BLOOD PROTEINS; CHROMATOGRAPHY, LIQUID; DRIED BLOOD SPOT TESTING; HUMANS; ISOTOPE LABELING; PEPTIDES; PROTEIN STABILITY; PROTEOMICS; REPRODUCIBILITY OF RESULTS; TANDEM MASS SPECTROMETRY;

EID: 84946012492     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.O115.049957     Document Type: Article

References (60)

1. McDade, T. W., Williams, S., and Snodgrass, J. J. (2007) What a Drop Can Do: Dried Blood Spots as a Minimally Invasive Method for Integrating Biomarkers into Population-Based Research. Demography 44, 899-925
2. Demirev, P. A. (2013) Dried blood spots: analysis and applications. Anal. Chem. 85, 779-789
3. Chace, D. H., Kalas, T. A., and Naylor, E. W. (2003) Use of tandem mass spectrometry for multianalyte screening of dried blood specimens from newborns. Clin. Chem. 49, 1797-1817
4. Lehotay, D. C., Hall, P., Lepage, J., Eichhorst, J. C., Etter, M. L., and Greenberg, C. R. (2011) LC-MS/MS progress in newborn screening. Clin. Biochem. 44, 21-31
5. Edelbroek, P. M., Van Der Heijden, J., and Stolk, L. M. L. (2009) Dried Blood Spot Methods in Therapeutic Drug Monitoring: Methods, Assays, and Pitfalls. Ther. Drug Monit. 31, 327-336
6. Wilhelm, A. J., Den Burger, J. C., and Swart, E. L. (2014) Therapeutic drug monitoring by dried blood spot: progress to date and future directions. Clin. Pharmacokinet. 53, 961-973
7. Stove, C. P., Ingels, A. S., De Kesel, P. M., and Lambert, W. E. (2012) Dried blood spots in toxicology: from the cradle to the grave? Critical Rev. Toxicol. 42, 230-243
8. Quraishi, R., Jain, R., and Ambekar, A. (2013) The Use of Dried Blood Spot Samples in Screening Drugs of Abuse. Pharmacol. Pharm. 4, 152-159
9. Snijdewind, I. J. M., Van Kampen, J. J. A., Fraaij, P. L. A., Van Der Ende, M. E., Osterhaus, A. D. M. E., and Gruters, R. A. (2012) Current and future applications of dried blood spots in viral disease management. Antiviral Research 93, 309-321
10. Johannessen, A. (2010) Dried blood spots in HIV monitoring: applications in resource-limited settings. Bioanalysis 2, 1893-1908
11. Lehmann, S., Delaby, C., Vialaret, J., Ducos, J., and Hirtz, C. (2013) Current and future use of "dried blood spot" analyses in clinical chemistry. Clin. Chem. Lab. Med. 51, 1897-1909
12. Addona, T. A., Abbatiello, S. E., Schilling, B., Skates, S. J., Mani, D. R., Bunk, D. M., Spiegelman, C. H., Zimmerman, L. J., Ham, A.-J. L., Keshishian, H., Hall, S. C., Allen, S., Blackman, R. K., Borchers, C. H., Buck, C., Cardasis, H. L., Cusack, M. P., Dodder, N. G., Gibson, B. W., Held, J. M., Hiltke, T., Jackson, A., Johansen, E. B., Kinsinger, C. R., Li, J., Mesri, M., Neubert, T. A., Niles, R. K., Pulsipher, T. C., Ransohoff, D., Rodriguez, H., Rudnick, P. A., Smith, D., Tabb, D. L., Tegeler, T. J., Variyath, A. M., Vega-Montoto, L. J., Wahlander, A., Waldemarson, S., Wang, M., Whiteaker, J. R., Zhao, L., Anderson, N. L., Fisher, S. J., Liebler, D. C., Paulovich, A. G., Regnier, F. E., Tempst, P., and Carr, S. A. (2009) Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotech. 27, 633-641
13. Boja, E. S., and Rodriguez, H. (2012) Mass spectrometry-based targeted quantitative proteomics: Achieving sensitive and reproducible detection of proteins. Proteomics 12, 1093-1110
14. Picotti, P., and Aebersold, R. (2012) Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat. Meth. 9, 555-566
15. Abbatiello, S. E., Schilling, B., Mani, D. R., Zimmerman, L. J., Hall, S. C., MacLean, B., Albertolle, M., Allen, S., Burgess, M. W., Cusack, M. P., Ghosh, M., Hedrick, V., Held, J. M., Inerowicz, H. D., Jackson, A., Keshishian, H., Kinsinger, C. R., Lyssand, J., Makowski, L., Mesri, M., Rodriguez, H., Rudnick, P., Sadowski, P., Sedransk, N., Shaddox, K., Skates, S. J., Kuhn, E., Smith, D., Whiteaker, J. R., Whitwell, C., Zhang, S., Borchers, C. H., Fisher, S. J., Gibson, B. W., Liebler, D. C., MacCoss, M. J., Neubert, T. A., Paulovich, A. G., Regnier, F. E., Tempst, P., and Carr, S. A. (2015) Large-scale inter-laboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma. Mol. Cell. Proteomics pii: mcp. M114.047050
16. Keevil, B. G. (2011) The analysis of dried blood spot samples using liquid chromatography tandem mass spectrometry. Clin. Biochem. 44, 110-118
17. Li, W., and Tse, F. L. S. (2010) Dried blood spot sampling in combination with LC-MS/MS for quantitative analysis of small molecules. Biomed. Chromatogr. 24, 49-65
18. Wagner, M., Tonoli, D., Varesio, E., and Hopfgartner, G. (2014) The use of mass spectrometry to analyze dried blood spots. Mass Spectrom. Rev. 9999, 1-78
19. Van Amsterdam, P., and Waldrop, C. (2010) The application of dried blood spot sampling in global clinical trials. Bioanalysis 2, 1783-1786
20. Burnett, J. E. C. (2011) Dried blood spot sampling: practical considerations and recommendation for use with preclinical studies. Bioanalysis 3, 1099-1107
21. Xu, Y., Woolf, E. J., Agrawal, N. G. B., Kothare, P., Pucci, V., and Bateman, K. P. (2013) Merck's perspective on the implementation of dried blood spot technology in clinical drug development - why, when and how. Bioanalysis 5, 341-350
22. Zukunft, S., Sorgenfrei, M., Prehn, C., Moller, G., and Adamski, J. (2013) Targeted Metabolomics of Dried Blood Spot Extracts. Chromatographia 76, 1295-1305
23. Martin, N. J., and Cooper, H. J. (2014) Challenges and opportunities in mass spectrometric analysis of proteins from dried blood spots. Expert Rev. Proteomics 11, 685-695
24. Daniel, Y. A., Turner, C., Haynes, R. M., Hunt, B. J., and Dalto, R. N. (2007) Quantification of Hemoglobin A2 by Tandem Mass Spectrometry. Clin. Chem. 53, 1448-1454
25. Boemer, F., Ketelslegers, O., Minon, J.-M., Bours, V., and Schoos, R. (2008) Newborn Screening for Sickle Cell Disease Using Tandem Mass Spectrometry. Clin. Chem. 54, 2036-2041
26. Boemer, F., Cornet, Y., Libioulle, C., Segers, K., Bours, V., and Schoos, R. (2011) 3-years experience review of neonatal screening for hemoglobin disorders using tandem mass spectrometry. Clin. Chim. Acta 412, 1476-1479
27. Moat, S. J., Rees, D., King, L., Ifederu, A., Harvey, K., Hall, K., Lloyd, G., Morrell, C., and Hillier, S. (2014) Newborn blood spot screening for sickle cell disease by using tandem mass spectrometry: implementation of a protocol to identify only the disease states of sickle cell disease. Clin. Chem. 60, 373-380
28. DeWilde, A., Sadilkova, K., Sadilek, M., Vasta, V., and Hahn, S. H. (2008) Tryptic Peptide Analysis of Ceruloplasmin in Dried Blood Spots Using Liquid Chromatography-Tandem Mass Spectrometry: Application to Newborn Screening. Clin. Chem. 54, 1961-1968
29. Cox, H. D., Rampton, J., and Eichner, D. (2013) Quantification of insulin-like growth factor-1 in dried blood spots for detection of growth hormone abuse in sport. Anal. Bioanal. Chem. 405, 1949-1958
30. Cox, H. D., Hughes, C. M., and Eichner, D. (2014) Sensitive quantification of IGF-1 and its synthetic analogs in dried blood spots. Bioanalysis 6, 2651-2662
31. Chambers, A. G., Percy, A. J., Yang, J., Camenzind, A. G., and Borchers, C. H. (2013) Multiplexed Quantitation of Endogenous Proteins in Dried Blood Spots by Multiple Reaction Monitoring Mass Spectrometry. Mol. Cell. Proteomics 12, 781-791
32. The-UniProt-Consortium (2015) UniProt: a hub for protein information. Nucleic Acids Res. 43, D204-D212
33. Percy, A. J., Yang, J., Chambers, A. G., Simon, R., Hardie, D. B., and Borchers, C. H. (2014) Multiplexed MRM with Internal Standards for Cerebrospinal Fluid Candidate Protein Biomarker Quantitation. J. Proteome Res. 13, 3733-3747
34. Domanski, D., Percy, A. J., Yang, J., Chambers, A. G., Hill, J. S., Cohen Freue, G. V., and Borchers, C. H. (2012) MRM-based Multiplexed Quantitation of 67 Putative Cardiovascular Disease Biomarkers in Human Plasma. Proteomics 12, 1222-1243
35. Percy, A. J., Chambers, A. G., Yang, J., Jackson, A. M., Domanski, D., Burkhart, J., Sickmann, A., and Borchers, C. H. (2013) Method and platform standardization in MRM-based quantitative plasma proteomics. J. Proteomics 95, 66-76
36. Percy, A. J., Yang, J., Hardie, D. B., Chambers, A. G., Tamura-Wells, J., and Borchers, C. H. (2015) Precise Quantitation of 136 Urinary Proteins by LC/MRM-MS using Stable Isotope Labeled Peptides as Internal Standards for Biomarker Discovery and/or Verification Studies. Methods 81, 24-33
37. Anderson, N. L. (2010) The clinical plasma proteome: a survey of clinical assays for proteins in plasma and serum. Clin. Chem. 56, 177-185
38. Kuzyk, M. A., Parker, C. E., Domanski, D., and Borchers, C. H. (2013) Development of MRM-based assays for the absolute quantitation of plasma proteins. Methods Mol. Biol. 1023, 53-82
39. Mohammed, Y., Domans̈ki, D., Jackson, A. M., Smith, D. S., Deelder, A. M., Palmblad, M., and Borchers, C. H. (2014) PeptidePicker: a scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments. J. Proteomics 106, 151-161
40. Mohammed, Y., Percy, A. J., Chambers, A. G., and Borchers, C. H. (2015) Qualis-SIS: Automated Standard Curve Generation and Quality Assessment for Multiplexed Targeted Quantitative Proteomic Experiments with Labeled Standards. J. Proteome Res. 14, 1137-1146
41. De Kesel, P. M., Sadones, N., Capiau, S., Lambert, W. E., and Stove, C. P. (2013) Hemato-critical issues in quantitative analysis of dried blood spots: challenges and solutions. Bioanalysis 5, 2023-2041
42. De Kesel, P. M., Capiau, S., Lambert, W. E., and Stove, C. P. (2014) Current strategies for coping with the hematocrit problem in dried blood spot analysis. Bioanalysis 6, 1871-1874
43. Li, F., Ploch, S., Fast, D., and Michael, S. (2012) Perforated dried blood spot accurate microsampling: the concept and its applications in toxicokinetic sample collection. J. Mass Spectrom. 47, 655-667
44. Miller, E. M., and McDade, T. W. (2012) A highly sensitive immunoassay for interleukin-6 in dried blood spots. Am. J. Hum. Biol. 24, 863-865
45. Whiteaker, J. R., Zhao, L., Anderson, L., and Paulovich, A. G. (2010) An Automated and Multiplexed Method for High Throughput Peptide Immunoaffinity Enrichment and Multiple Reaction Monitoring Mass Spectrometrybased Quantification of Protein Biomarkers. Mol. Cell. Proteomics 9, 184-196
46. Shi, T., Su, D., Liu, T., Tang, K., Camp, D. G., Qian, W. J., and Smith, R. D. (2012) Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics. Proteomics 12, 1074-1092
47. Percy, A. J., Simon, R., Chambers, A. G., and Borchers, C. H. (2014) Enhanced Sensitivity and Multiplexing with 2D LC/MRM-MS and Labeled Standards for Deeper and More Comprehensive Protein Quantitation. J. Proteomics 106, 113-124
48. Keshishian, H., Addona, T., Burgess, M., Kuhn, E., and Carr, S. A. (2007) Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics 6, 2212-2229
49. Kennedy, J. J., Abbatiello, S. E., Kim, K., Yan, P., Whiteaker, J. R., Lin, C., Kim, J. S., Zhang, Y., Wang, X., Ivey, R. G., Zhao, L., Min, H., Lee, Y. H., Yu, M. H., Yang, E. G., Lee, C., Wang, P., Rodriguez, H., Kim, Y., Carr, S. A., and Paulovich, A. G. (2014) Demonstrating the feasibility of largescale development of standardized assays to quantify human proteins. Nature Meth. 11, 149-155
50. Arsene, C. G., Ohlendorf, R., Burkitt, W., Pritchard, C., Henrion, A., O'Connor, G., Bunk, D. M., and Güttler, B. (2008) Protein quantification by isotope dilution mass spectrometry of proteolytic fragments: cleavage rate and accuracy. Anal. Chem. 80, 4154-4160
51. Brownridge, P., and Beynon, R. J. (2011) The importance of the digest: proteolysis and absolute quantification in proteomics. Methods 54, 351-360
52. Brun, V., Masselon, C., Garin, J., and Dupuis, A. (2009) Isotope dilution strategies for absolute quantitative proteomics. J. Proteomics 72, 740-749
53. Carr, S. A., Abbatiello, S. E., Ackermann, B. L., Borchers, C., Domon, B., Deutsch, E. W., Grant, R. P., Hoofnagle, A. N., Huumlttenhain, 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., 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., and Weintraub, S. (2014) Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometrybased Assay Development Using a Fit-for-Purpose Approach. Mol. Cell. Proteomics 13, 907-917
54. Hoofnagle, A. N., Becker, J. O., Oda, M. N., Cavigiolio, G., Mayer, P., and Vaisar, T. (2012) Multiple-reaction monitoring-mass spectrometric assays can accurately measure the relative protein abundance in complex mixtures. Clin. Chem. 58, 777-778
55. Percy, A. J., Chambers, A. G., Yang, J., Hardie, D. B., and Borchers, C. H. (2014) Advances in multiplexed MRM-based protein biomarker quantitation toward clinical utility. Biochim. Biophys. Acta 1844, 917-926
56. Bowen, C. L., Dopson, W., Kemp, D. C., Lewis, M., Lad, R., and Overvold, C. (2011) Investigations into the environmental conditions experienced during ambient sample transport: impact to dried blood spot sample shipments. Bioanalysis 3, 1625-1633
57. Emmons, G., and Rowland, M. (2010) Pharmacokinetic considerations as to when to use dried blood spot sampling. Bioanalysis 2, 1791-1796
58. 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., and Qian, W. J. (2013) Targeted Quantification of Low ng/mL Level Proteins in Human Serum without Immunoaffinity Depletion. J. Proteome Res. 12, 3353-3361
59. Whiteaker, J. R., Lin, C., Kennedy, J., Hou, L., Trute, M., Sokal, I., Yan, P., Schoenherr, R. M., Zhao, L., Voytovich, U. J., Kelly-Spratt, K. S., Krasnoselsky, A., Gafken, P. R., Hogan, J. M., Jones, L. A., Wang, P., Amon, L., Chodosh, L. A., Nelson, P. S., McIntosh, M. W., Kemp, C. J., and Paulovich, A. G. (2011) A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat. Biotech. 29, 625-634
60. Schoenherr, R. M., Saul, R. G., Whiteaker, J. R., Yan, P., Whiteley, G. R., and Paulovich, A. G. (2015) Anti-peptide monoclonal antibodies generated for immuno-multiple reaction monitoring-mass spectrometry assays have a high probability of supporting Western blot and ELISA. Mol. Cell. Proteomics 14, 382-398