ABSTRACT
In the aftermath of the successful completion of the sequencing of the human genome, which highlighted the surprising fact that humans have only approximately 20,000-25,000 protein-coding genes [1], hardly enough to explain the complexity gap between humans and the lowly round worm
14.1 Introduction ................................................................................................ 313 14.2 The Reconfi gurable Computing Paradigm ............................................ 315 14.3 Protein Identifi cation by Sequence Database Searching Using
Mass Spectral Fingerprints ....................................................................... 317 14.3.1 Overview of the Approach ........................................................... 317 14.3.2 Abstract Computational Model ................................................... 318 14.3.3 Cleavage Rules ............................................................................... 318 14.3.4 Protein Identifi cation by Spectral Matching .............................. 321
14.4 Reconfi gurable Computing Platform ...................................................... 322 14.5 Protein Sequence Database FPGA Search Engine ................................ 325
14.5.1 Database Encoding ........................................................................ 325 14.5.2 Database Search Processor ........................................................... 326
14.5.2.1 Digestion Unit .................................................................. 326 14.5.2.2 Variable Modifi cations ................................................... 327 14.5.2.3 Scoring Unit ..................................................................... 328
14.6 Performance Evaluation ............................................................................ 331 14.7 References ...................................................................................................333
