Anti-peptide monoclonal antibodies generated for immuno-multiple reaction monitoring-mass spectrometry assays have a high probability of supporting western blot and ELISA

Molecular and Cellular Proteomics

Volumn 14, Issue 2, 2015, Pages 382-398

  Schoenherr, Regine M ^a   Saul, Richard G ^b   Whiteaker, Jeffrey R ^a   Yan, Ping ^a   Whiteley, Gordon R ^b   Paulovich, Amanda G ^a  

^a Fred Hutchinson Cancer Research Center   (United States)

^b FREDERICK NATIONAL LABORATORY FOR CANCER RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIGEN; MONOCLONAL ANTIBODY; PEPTIDE ANTIBODY; REAGENT; DYES, REAGENTS, INDICATORS, MARKERS AND BUFFERS; PEPTIDE; RECOMBINANT PROTEIN;

AMINO ACID SEQUENCE; ANALYTIC METHOD; ANIMAL CELL; ANIMAL EXPERIMENT; ANTIBODY AFFINITY; ARTICLE; CONTROLLED STUDY; ENZYME LINKED IMMUNOSORBENT ASSAY; MASS SPECTROMETRY; NEW ZEALAND WHITE (RABBIT); NONHUMAN; PRIORITY JOURNAL; PROBABILITY; PROTEIN EXPRESSION; QUANTITATIVE ANALYSIS; TECHNOLOGY; VALIDATION PROCESS; WESTERN BLOTTING; ANIMAL; CHEMISTRY; HUMAN; HYBRIDOMA; IMMUNOLOGY; METABOLISM; MOLECULAR GENETICS; PROCEDURES; RABBIT; REPRODUCIBILITY;

AMINO ACID SEQUENCE; ANIMALS; ANTIBODIES, MONOCLONAL; BLOTTING, WESTERN; ENZYME-LINKED IMMUNOSORBENT ASSAY; HUMANS; HYBRIDOMAS; INDICATORS AND REAGENTS; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PEPTIDES; RABBITS; RECOMBINANT PROTEINS; REPRODUCIBILITY OF RESULTS;

EID: 84921908838     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.O114.043133     Document Type: Article

References (36)

1. Hoofnagle, A. N., and Wener, M. H. (2009) The fundamental flaws of immunoassays and potential solutions using tandem mass spectrometry. J. Immunol. Methods 347, 3-11
2. Gillette, M. A., and Carr, S. A. (2013) Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry. Nat. Methods 10, 28-34
3. Picotti, P., Bodenmiller, B., and Aebersold, R. (2013) Proteomics meets the scientific method. Nat. Methods 10, 24-27
4. 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., 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 large-scale development of standardized assays to quantify human proteins. Nat. Methods 11, 149-155
5. 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., 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. Biotechnol. 27, 633-641
6. Wang, P., Whiteaker, J. R., and Paulovich, A. G. (2009) The evolving role of mass spectrometry in cancer biomarker discovery. Cancer Biol. Ther. 8, 1083-1094
7. Paulovich, A. G., Whiteaker, J. R., Hoofnagle, A. N., and Wang, P. (2008) The interface between biomarker discovery and clinical validation: the tar pit of the protein biomarker pipeline. Proteomics Clin. Appl. 2, 1386-1402
8. Anderson, N. L., Anderson, N. G., Haines, L. R., Hardie, D. B., Olafson, R. W., and Pearson, T. W. (2004) Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J. Proteome Res. 3, 235-244
9. Kuhn, E., Addona, T., Keshishian, H., Burgess, M., Mani, D. R., Lee, R. T., Sabatine, M. S., Gerszten, R. E., and Carr, S. A. (2009) Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry. Clin. Chem. 55, 1108-1117
10. 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. Biotechnol. 29, 625-634
11. Schoenherr, R. M., Whiteaker, J. R., Zhao, L., Ivey, R. G., Trute, M., Kennedy, J., Voytovich, U. J., Yan, P., Lin, C., and Paulovich, A. G. (2012) Multiplexed quantification of estrogen receptor and HER2/Neu in tissue and cell lysates by peptide immunoaffinity enrichment mass spectrometry. Proteomics 12, 1253-1260
12. Whiteaker, J. R., and Paulovich, A. G. (2011) Peptide immunoaffinity enrichment coupled with mass spectrometry for peptide and protein quantification. Clin. Lab. Med. 31, 385-396
13. Zhao, L., Whiteaker, J. R., Pope, M. E., Kuhn, E., Jackson, A., Anderson, N. L., Pearson, T. W., Carr, S. A., and Paulovich, A. G. (2011) Quantification of proteins using peptide immunoaffinity enrichment coupled with mass spectrometry. J. Vis. Exp. 53, doi: 10.3791/2812
14. Anderson, N. L., Anderson, N. G., Pearson, T. W., Borchers, C. H., Paulovich, A. G., Patterson, S. D., Gillette, M., Aebersold, R., and Carr, S. A. (2009) A human proteome detection and quantitation project. Mol. Cell. Proteomics 8, 883-886
15. Whiteaker, J. R., Zhao, L., Lin, C., Yan, P., Wang, P., and Paulovich, A. G. (2012) Sequential multiplexed analyte quantification using peptide immunoaffinity enrichment coupled to mass spectrometry. Mol. Cell. Proteomics 11, M111 015347
16. 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 spectrometry-based quantification of protein biomarkers. Mol. Cell. Proteomics 9, 184-196
17. Kuhn, E., Whiteaker, J. R., Mani, D. R., Jackson, A. M., Zhao, L., Pope, M. E., Smith, D., Rivera, K. D., Anderson, N. L., Skates, S. J., Pearson, T. W., Paulovich, A. G., and Carr, S. A. (2012) Interlaboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma. Mol. Cell. Proteomics 11, M111 013854
18. Nilsson, P., Paavilainen, L., Larsson, K., Odling, J., Sundberg, M., Andersson, A. C., Kampf, C., Persson, A., Al-Khalili Szigyarto, C., Ottosson, J., Bjorling, E., Hober, S., Wernerus, H., Wester, K., Ponten, F., and Uhlen, M. (2005) Towards a human proteome atlas: high-throughput generation of mono-specific antibodies for tissue profiling. Proteomics 5, 4327-4337
19. Trier, N. H., Hansen, P. R., and Houen, G. (2012) Production and characterization of peptide antibodies. Methods 56, 136-144
20. Razavi, M., Pope, M. E., Soste, M. V., Eyford, B. A., Jackson, A. M., Anderson, N. L., and Pearson, T. W. (2011) MALDI immunoscreening (MiSCREEN): a method for selection of anti-peptide monoclonal antibodies for use in immunoproteomics. J. Immunol. Methods 364, 50-64
21. Schoenherr, R. M., Zhao, L., Whiteaker, J. R., Feng, L. C., Li, L., Liu, L., Liu, X., and Paulovich, A. G. (2010) Automated screening of monoclonal antibodies for SISCAPA assays using a magnetic bead processor and liquid chromatography-selected reaction monitoring-mass spectrometry. J. Immunol. Methods 353, 49-61
22. MacLean, B., Tomazela, D. M., Abbatiello, S. E., Zhang, S., Whiteaker, J. R., Paulovich, A. G., Carr, S. A., and MacCoss, M. J. (2010) Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry. Anal. Chem. 82, 10116-10124
23. MacLean, B., Tomazela, D. M., Shulman, N., Chambers, M., Finney, G. L., Frewen, B., Kern, R., Tabb, D. L., Liebler, D. C., and MacCoss, M. J. (2010) Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26, 966-968
24. Whiteaker, J. R., Halusa, G. N., Hoofnagle, A. N., Sharma, V., MacLean, B., Yan, P., Wrobel, J. A., Kennedy, J., Mani, D. R., Zimmerman, L. J., Meyer, M. R., Mesri, M., Rodriguez, H., Clinical Proteomic Tumor Analysis Consortium (CPTAC), and Paulovich, A. G. (2014) CPTAC Assay Portal: a repository of targeted proteomic assays. Nat. Methods 11, 703-704
25. Ellis, M. J., Gillette, M., Carr, S. A., Paulovich, A. G., Smith, R. D., Rodland, K. K., Townsend, R. R., Kinsinger, C., Mesri, M., Rodriguez, H., Liebler, D. C., and Clinical Proteomic Tumor Analysis Consortium (CPTAC) (2013) Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium. Cancer Discov. 3, 1108-1112
26. Chung, J.-Y., Lee, S.-J., Kris, Y., Braunschweig, T., Traicoff, J. L., and Hewitt, S. M. (2008) A well-based reverse-phase protein array applicable to extracts from formalin-fixed paraffin-embedded tissue. Proteomics Clin. Appl. 2, 1539-1547
27. 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., and Weintraub, S. (2014) Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol. Cell. Proteomics 13, 907-917
28. Yao, B., Zheng, D., Liang, S., and Zhang, C. (2013) Conformational B-cell epitope prediction on antigen protein structures: a review of current algorithms and comparison with common binding site prediction methods. PLoS One 8, e62249
29. Whiteaker, J. R., Zhao, L., Zhang, H. Y., Feng, L. C., Piening, B. D., Anderson, L., and Paulovich, A. G. (2007) Antibody-based enrichment of peptides on magnetic beads for mass-spectrometry-based quantification of serum biomarkers. Anal. Biochem. 362, 44-54
30. Hoofnagle, A. N., Becker, J. O., Wener, M. H., and Heinecke, J. W. (2008) Quantification of thyroglobulin, a low-abundance serum protein, by immunoaffinity peptide enrichment and tandem mass spectrometry. Clin. Chem. 54, 1796-1804
31. Neubert, H., Gale, J., and Muirhead, D. (2010) Online high-flow peptide immunoaffinity enrichment and nanoflow LC-MS/MS: assay development for total salivary pepsin/pepsinogen. Clin. Chem. 56, 1413-1423
32. Razavi, M., Frick, L. E., LaMarr, W. A., Pope, M. E., Miller, C. A., Anderson, N. L., and Pearson, T. W. (2012) High-throughput SISCAPA quantitation of peptides from human plasma digests by ultrafast, liquid chromatography-free mass spectrometry. J. Proteome Res. 11, 5642-5649
33. Neubert, H., Muirhead, D., Kabir, M., Grace, C., Cleton, A., and Arends, R. (2013) Sequential protein and peptide immunoaffinity capture for mass spectrometry-based quantification of total human beta-nerve growth factor. Anal. Chem. 85, 1719-1726
34. Zhao, Y., Widen, S. G., Jamaluddin, M., Tian, B., Wood, T. G., Edeh, C. B., and Brasier, A. R. (2011) Quantification of activated NF-kappaB/RelA complexes using ssDNA aptamer affinity-stable isotope dilution-selected reaction monitoring-mass spectrometry. Mol. Cell. Proteomics 10, M111 008771
35. Whiteaker, J. R., Zhao, L., Frisch, C., Ylera, F., Harth, S., Knappik, A., and Paulovich, A. G. (2014) High-affinity recombinant antibody fragments (Fabs) can be applied in peptide enrichment immuno-MRM assays. J. Proteome Res. 13, 2187-2196
36. Seeber, S., Ros, F., Thorey, I., Tiefenthaler, G., Kaluza, K., Lifke, V., Fischer, J. A., Klostermann, S., Endl, J., Kopetzki, E., Pashine, A., Siewe, B., Kaluza, B., Platzer, J., and Offner, S. (2014) A robust high throughput platform to generate functional recombinant monoclonal antibodies using rabbit B cells from peripheral blood. PLoS One 9, e86184