Scientific Publications

Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry.

Publication TypeJournal Article
AuthorsWhiteaker, JR, Zhao L., Abbatiello SE, Burgess M., Kuhn E., Lin C., Pope ME, Razavi M., Anderson NL, Pearson TW, Carr SA, and Paulovich AG
AbstractStable isotope standards and capture by antipeptide antibodies (SISCAPA) couples affinity enrichment of peptides with stable isotope dilution and detection by multiple reaction monitoring mass spectrometry to provide quantitative measurement of peptides as surrogates for their respective proteins. In this report, we describe a feasibility study to determine the success rate for production of suitable antibodies for SISCAPA assays in order to inform strategies for large-scale assay development. A workflow was designed that included a multiplex immunization strategy in which up to five proteotypic peptides from a single protein target were used to immunize individual rabbits. A total of 403 proteotypic tryptic peptides representing 89 protein targets were used as immunogens. Antipeptide antibody titers were measured by ELISA and 220 antipeptide antibodies representing 89 proteins were chosen for affinity purification. These antibodies were characterized with respect to their performance in SISCAPA-multiple reaction monitoring assays using trypsin-digested human plasma matrix. More than half of the assays generated were capable of detecting the target peptide at concentrations of less than 0.5 fmol/μl in human plasma, corresponding to protein concentrations of less than 100 ng/ml. The strategy of multiplexing five peptide immunogens was successful in generating a working assay for 100% of the targeted proteins in this evaluation study. These results indicate it is feasible for a single laboratory to develop hundreds of assays per year and allow planning for cost-effective generation of SISCAPA assays.
Year of Publication2011
JournalMolecular & cellular proteomics : MCP
Volume10
Issue4
PagesM110.005645
Date Published (YYYY/MM/DD)2011/04/01
ISSN Number1535-9476
DOI10.1074/mcp.M110.005645
PubMedhttp://www.ncbi.nlm.nih.gov/pubmed/21245105?dopt=Abstract