ABSTRACT
I. INTRODUCTION Although the value of genomics is indisputable, the need to study protein expression directly has become obvious. First, the only way to determine that an open reading frame encodes a protein is to identify that protein in a biological sample. Moreover, the paradigm of ‘‘one gene, one protein’’ has long been dismissed, with the discovery of alternative splicing, mRNA editing, and posttranslational modification. As there is a lack of correlation between transcription profiles and cellular protein levels, proteomics measures the proteins-those molecules directly involved in the cellular processes (additional commentary on these points can be found in Refs. 1-3). Fulfillment of the promise of proteomics depends on the power of the assays used to probe the proteome. Analysis of the proteome is a far more daunting task than analysis of the genome, as proteins are more complex than DNA and no protein amplification technique exists that is analogous to polymerase chain reaction (PCR). To successfully mine the cellular proteome, researchers must utilize multiple strategies while remaining cognizant of the respective strengths and weaknesses of each approach and, ultimately, with the intent to integrate the data obtained from these strategies into the underlying biology of the cellular system under investigation. Although critics of genomic and proteomic approaches to biological investigation decry the absence of hypothesis testing inherent to these methods, we maintain that these strategies have the potential to provide valuable information not readily attained using traditional ‘‘one gene/protein at a time’’ approaches. However, successful use of these strategies requires careful experimental design and the development of new and innovative approaches for high-throughput protein analysis.
