Mass spectrometry allows direct identification of proteins in large genomes

Proteome projects seek to provide systematic functional analysis of the gen es uncovered by genome sequencing initiatives. Mass spectrometric protein i dentification is a key requirement in these studies but to date, database s earching tools rely on the availability of protein sequences derived from f ull length cDNA, expressed sequence tags or predicted open reading frames ( ORFs) from genomic sequences. We demonstrate here that proteins can be iden tified directly in large genomic databases using peptide sequence tags obta ined by tandem mass spectrometry. On the background of vast amounts of nonc oding DNA sequence, identified peptides localize coding sequences (exons) i n a confined region of the genome, which contains the cognate gene. The app roach does not require prior information about putative ORFs as predicted b y computerized gene finding algorithms. The method scales to the complete h uman genome and allows identification, mapping, cloning and assistance in g ene prediction of any protein for which minimal mass spectrometric informat ion can be obtained. Several novel proteins from Arabidopsis thaliana and h uman have been discovered in this way.