Pharmaceutical Sciences Faculty Publications

Identification of the SELDI ProteinChip Human Serum Retentate by Microcapillary Liquid Chromatography-Tandem Mass Spectrometry

Document Type

Article

Publication Date

9-1-2006

Journal Title

Journal of Proteome Research

ISSN

1535-3893

Volume

5

Issue

9

First Page

2207

Last Page

2216

DOI

10.1021/pr060061h

PubMed ID

16944932

Abstract

Surface-enhanced laser desorption/ionization (SELDI) time-of-flight (TOF) mass spectrometry (MS) has been widely applied for conducting biomarker research with the goal of discovering patterns of proteins and/or peptides from biological samples that reflect disease status. Many diseases, ranging from cancers of the colon, breast, and prostate to Alzheimer's disease, have been studied through serum protein profiling using SELDI-based methods. Although the results from SELDI-based diagnostic studies have generated a great deal of excitement and skepticism alike, the basis of the molecular identities of the features that underpin the diagnostic potential of the mass spectra is still largely unexplored. A detailed investigation has been undertaken to identify the compliment of serum proteins that bind to the commonly used weak cation exchange (WCX-2) SELDI protein chip. Following incubation and washing of a standard serum sample on the WCX-2 sorbent, proteins were harvested, digested with trypsin, fractionated by strong cation exchange liquid chromatography (LC), and subsequently analyzed by microcapillary reversed-phase LC coupled online with an ion-trap mass spectrometer. This analysis resulted in the identification of 383 unique proteins in the WCX-2 serum retentate. Among the proteins identified, 50 (13%) are documented clinical biomarkers with 36 of these (72%) identified from multiple peptides.

Keywords

Biomarkers, blood proteins, chromatography, ion exchange, humans, protein array analysis, proteomics, spectrometry, mass

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