Strategies for Discovery and Characterization of Novel Biomarkers Using SELDI Technology

Abstract

Successful biomarker discovery and development efforts require a working knowledge of multiple disciplines, including study and experimental design, proteomics technologies, and data analysis and interpretation. There are two general proteomic approaches to biomarker discovery: top-down and bottom-up methodologies. In bottom-up methods, complex samples are digested with a protease (typically trypsin) and subjected to an LC separation prior to analysis in a tandem mass spectrometer. In contrast, Bio-Rad's biomarker workflow focuses on native proteins and peptides top-down proteomics. This approach preserves information about post-translational modifications (truncation, glycosylation, etc.) that may be important indications of disease. Bio-Rad's Biomarker Research Center has years of expertise in addressing and circumventing common issues associated with biomarker attrition through their collaborative research services. SELDI-based biomarker studies can typically be divided into four phases: Discovery, Validation, Purification and Identification, and Assay Development, each of which requires a unique approach. The discovery phase is characterized by analyzing samples under a large set of experimental profiling conditions. An initial panel of candidate biomarkers is obtained, which is then tested during the validation phase. In the discovery and validation phases, it is especially important to optimize study design and statistical methods to avoid pre-analytical bias and yield robust markers. Identification can be performed at the end of the discovery phase or at any point during the validation phase, and generally requires standard protein purification procedures (column chromatography, size filtration, SDS-PAGE, etc.), followed by protease digestion and sequence analysis on a tandem mass spectrometer. Identification of the biomarkers facilitates the development of analyte specific assays and provides insight into the disease biology. Once the biomarkers have been positively identified, quantitati ve assays doi:10.4172/jpb.s1000200 Journal of Proteomics & Bioinformatics Open Access www.omicsonline.com Abstract No.329 JPB/Vol.S2/July 2008/Special Issue Proceedings of The Joint 2 Pacific Rim International Conference on Protein Science and 4 Asian-Oceania Human Proteome Organization, CairnsAustralia, 22-26 June 2008 J Proteomics Bioinform Volume S2:280-281(2008) ISSN:0974-276X JPB, an open access journal can be developed for routine testing on an appropriate immunoassay platform. SELDI-based immunoassays are particularly useful for detecting biomarkers with post-translational modifications. Approaches to optimizing biomarker workflows to deliver robust biomarkers and biomarker assays will be discussed using examples from Biomarker Research Center collaborations.