Immunoproteomics using polyclonal antibodies and stable isotope-labeled affinity-purified recombinant proteins

Molecular and Cellular Proteomics

Volumn 13, Issue 6, 2014, Pages 1611-1624

  Edfors, Fredrik ^a   Boström, Tove ^a   Forsström, Björn ^a   Zeiler, Marlis ^b   Johansson, Henrik ^c   Lundberg, Emma ^a   Hober, Sophia ^a   Lehtiö, Janne ^c   Mann, Matthias ^b   Uhlen, Mathias ^a  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^b MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^c SCIENCE FOR LIFE LABORATORY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

POLYCLONAL ANTIBODY; PROTEIN A; PROTEOME; RECOMBINANT PROTEIN; STABLE ISOTOPE; TRYPSIN; ANTIBODY; EPITOPE; TUMOR PROTEIN;

ACCURACY; ANALYTIC METHOD; ARTICLE; CELL LYSATE; EPITOPE MAPPING; HELA CELL LINE; HUMAN; HUMAN CELL; IMMUNIZATION; IMMUNOPROTEOMICS; ISOTOPE LABELING; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEOMICS; QUANTITATIVE ANALYSIS; BIOSYNTHESIS; GENE EXPRESSION REGULATION; IMMUNOLOGY; ISOLATION AND PURIFICATION; LIQUID CHROMATOGRAPHY; PROCEDURES;

ANTIBODIES; CHROMATOGRAPHY, LIQUID; EPITOPES; GENE EXPRESSION REGULATION, NEOPLASTIC; HELA CELLS; HUMANS; ISOTOPE LABELING; MASS SPECTROMETRY; NEOPLASM PROTEINS; PROTEOMICS; RECOMBINANT PROTEINS;

EID: 84901952830     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M113.034140     Document Type: Article

References (44)

1. Bjorhall, K., Miliotis, T., and Davidsson, P. (2005) Comparison of different depletion strategies for improved resolution in proteomic analysis of human serum samples. Proteomics 5, 307-317 (Pubitemid 40189661)
2. Steel, L. F., Trotter, M. G., Nakajima, P. B., Mattu, T. S., Gonye, G., and Block, T. (2003) Efficient and specific removal of albumin from human serum samples. Mol. Cell. Proteomics 2, 262-270
3. Jin, W. H., Dai, J., Li, S. J., Xia, Q. C., Zou, H. F., and Zeng, R. (2005) Human plasma proteome analysis by multidimensional chromatography prefractionation and linear ion trap mass spectrometry identification. J. Proteome Res. 4, 613-619 (Pubitemid 40548171)
4. Pieper, R., Gatlin, C. L., Makusky, A. J., Russo, P. S., Schatz, C. R., Miller, S. S., Su, Q., McGrath, A. M., Estock, M. A., Parmar, P. P., Zhao, M., Huang, S. T., Zhou, J., Wang, F., Esquer-Blasco, R., Anderson, N. L., Taylor, J., and Steiner, S. (2003) The human serum proteome: display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins. Proteomics 3, 1345-1364 (Pubitemid 36929557)
5. Pernemalm, M., Lewensohn, R., and Lehtio, J. (2009) Affinity prefractionation for MS-based plasma proteomics. Proteomics 9, 1420-1427
6. Berna, M., Ott, L., Engle, S., Watson, D., Solter, P., and Ackermann, B. (2008) Quantification of NTproBNP in rat serum using immunoprecipitation and LC/MS/MS: a biomarker of drug-induced cardiac hypertrophy. Anal. Chem. 80, 561-566 (Pubitemid 351206841)
7. 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 (Pubitemid 38500990)
8. Whiteaker, J. R., Zhao, L., Abbatiello, S. E., Burgess, M., Kuhn, E., Lin, C., Pope, M. E., Razavi, M., Anderson, N. L., Pearson, T. W., Carr, S. A., and Paulovich, A. G. (2011) Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry. Mol. Cell. Proteomics 10, M110.005645
9. 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
10. 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
11. Ahn, Y. H., Lee, J. Y., Lee, J. Y., Kim, Y. S., Ko, J. H., and Yoo, J. S. (2009) Quantitative analysis of an aberrant glycoform of TIMP1 from colon cancer serum by L-PHA-enrichment and SISCAPA with MRM mass spectrometry. J. Proteome Res. 8, 4216-4224
12. 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
13. Anderson, N. L., Jackson, A., Smith, D., Hardie, D., Borchers, C., and Pearson, T. W. (2009) SISCAPA peptide enrichment on magnetic beads using an in-line bead trap device. Mol. Cell. Proteomics 8, 995-1005
14. 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 (Pubitemid 46198803)
15. 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
16. Barr, J. R., Maggio, V. L., Patterson, D. G., Jr., Cooper, G. R., Henderson, L. O., Turner, W. E., Smith, S. J., Hannon, W. H., Needham, L. L., and Sampson, E. J. (1996) Isotope dilution-mass spectrometric quantification of specific proteins: model application with apolipoprotein A-I. Clin. Chem. 42, 1676-1682 (Pubitemid 26354748)
17. Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., and Gygi, S. P. (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. U.S.A. 100, 6940-6945 (Pubitemid 36706372)
18. Brun, V., Dupuis, A., Adrait, A., Marcellin, M., Thomas, D., Court, M., Vandenesch, F., and Garin, J. (2007) Isotope-labeled protein standards: toward absolute quantitative proteomics. Mol. Cell. Proteomics 6, 2139-2149
19. Singh, S., Springer, M., Steen, J., Kirschner, M. W., and Steen, H. (2009) FLEXIQuant: a novel tool for the absolute quantification of proteins, and the simultaneous identification and quantification of potentially modified peptides. J. Proteome Res. 8, 2201-2210
20. Zeiler, M., Straube, W. L., Lundberg, E., Uhlen, M., and Mann, M. (2012) A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines. Mol. Cell. Proteomics 11, O111.009613
21. Uhlen, M., Oksvold, P., Fagerberg, L., Lundberg, E., Jonasson, K., Forsberg, M., Zwahlen, M., Kampf, C., Wester, K., Hober, S., Wernerus, H., Bjorling, L., and Ponten, F. (2010) Towards a knowledge-based Human Protein Atlas. Nat. Biotechnol. 28, 1248-1250
22. Berglund, L., Bjorling, E., Jonasson, K., Rockberg, J., Fagerberg, L., Al-Khalili Szigyarto, C., Sivertsson, A., and Uhlen, M. (2008) A whole-genome bioinformatics approach to selection of antigens for systematic antibody generation. Proteomics 8, 2832-2839
23. Agaton, C., Falk, R., Hoiden Guthenberg, I., Gostring, L., Uhlen, M., and Hober, S. (2004) Selective enrichment of monospecific polyclonal antibodies for antibody-based proteomics efforts. J. Chromatogr. A 1043, 33-40 (Pubitemid 38952773)
24. Wisniewski, J. R., Zougman, A., Nagaraj, N., and Mann, M. (2009) Universal sample preparation method for proteome analysis. Nat. Methods 6, 359-362
25. Tegel, H., Steen, J., Konrad, A., Nikdin, H., Pettersson, K., Stenvall, M., Tourle, S., Wrethagen, U., Xu, L., Yderland, L., Uhlen, M., Hober, S., and Ottosson, J. (2009) High-throughput protein production - lessons from scaling up from 10 to 288 recombinant proteins per week. Biotechnol. J. 4, 51-57
26. Matic, I., Jaffray, E. G., Oxenham, S. K., Groves, M. J., Barratt, C. L., Tauro, S., Stanley-Wall, N. R., and Hay, R. T. (2011) Absolute SILAC-compatible expression strain allows Sumo-2 copy number determination in clinical samples. J. Proteome Res. 10, 4869-4875
27. Studier, F. W. (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr. Purif. 41, 207-234
28. Craig, R., and Beavis, R. C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466-1467 (Pubitemid 38931421)
29. Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392 (Pubitemid 35215372)
30. Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646-4658 (Pubitemid 37082259)
31. Han, D. K., Eng, J., Zhou, H., and Aebersold, R. (2001) Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 19, 946-951 (Pubitemid 32947573)
32. Scherer, W. F., Syverton, J. T., and Gey, G. O. (1953) Studies on the propagation in vitro of poliomyelitis viruses. IV. Viral multiplication in a stable strain of human malignant epithelial cells (strain HeLa) derived from an epidermoid carcinoma of the cervix. J. Exp. Med. 97, 695-710
33. Wisniewski, J. R., Zougman, A., and Mann, M. (2009) Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J. Proteome Res. 8, 5674-5678
34. Cox, J., and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367-1372
35. Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., and Mann, M. (2011) Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10, 1794-1805
36. 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
37. Stoevesandt, O., and Taussig, M. J. (2012) European and international collaboration in affinity proteomics. Nat. Biotechnol. 29, 511-514
38. Uhlen, M., Hultman, T., Wahlberg, J., Lundeberg, J., Bergh, S., Pettersson, B., Holmberg, A., Stahl, S., and Moks, T. (1992) Semi-automated solid-phase DNA sequencing. Trends Biotechnol. 10, 52-55
39. Mirzaei, H., and Regnier, F. (2006) Enhancing electrospray ionization efficiency of peptides by derivatization. Anal. Chem. 78, 4175-4183 (Pubitemid 43927413)
40. Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Paabo, S., and Mann, M. (2011) Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Syst. Biol. 7, 548
41. Glatter, T., Ludwig, C., Ahrne, E., Aebersold, R., Heck, A. J., and Schmidt, A. (2012) Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion. J. Proteome Res. 11, 5145-5156
42. Danielsson, F., Wiking, M., Mahdessian, D., Skogs, M., Ait Blal, H., Hjelmare, M., Stadler, C., Uhlen, M., and Lundberg, E. (2013) RNA deep sequencing as a tool for selection of cell lines for systematic subcellular localization of all human proteins. J. Proteome Res. 12, 299-307
43. Bjorling, E., and Uhlen, M. (2008) Antibodypedia, a portal for sharing antibody and antigen validation data. Mol. Cell. Proteomics 7, 2028-2037
44. Malm et al. (2014), unpublished