Abstract
| I. | Introduction | 25 |
| | A. A Brief History of Computer Application in Protein Sequence Analysis | 25 |
| | B. Requirements of Current Proteomics Research | 26 |
| | C. Mass Spectrometry Applications in Proteomics | 26 |
| II. | Basics of Transcriptional Regulation | 26 |
| | A. How Is Transcriptional Coregulation Achieved? | 26 |
| | B. Promoters and Transcription Complexes | 27 |
| III. | Synergisms Between Gene Regulation and Mass Spectrometry‐Based Proteomics | 29 |
| | A. Expression Array‐Based Gene Selection | 29 |
| | B. Protein Data‐Driven Coregulation Analysis | 30 |
| | C. A Practical Application Example | 30 |
| IV. | Conclusions | 30 |
| Acknowledgments | 32 |
| References | 32 |
Protein analysis is a field of research with a long history. Recently, the development of a series of proteomics approaches, i.e., simultaneous analyses on all or a majority of proteins in a cell at a given state, has reinvigorated protein analyses. Mass Spectrometry also developed into one of the most versatile technical tools supporting or even enabling many proteomics‐oriented approaches, providing a convenient link between experimental protein analysis and the corresponding amino acid sequences. Thus direct links to the genomic sequence can be established, which opens the door for a synergistic combination with genomic sequence analysis. This review focuses especially on aspects of genome‐wide transcription control, regulomics in analogy to all the other ‐omics, and how a combination of MS‐based proteomics with in silico regulomics analyses can produce synergistic effects in the quest to understand how cells function. This is illustrated on a real life example showing how the MS‐analysis and in silico promoter analysis can extend the list of candidates for signaling pathways, here the MAP kinase pathway. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 23:25–33, 2004