Strategy for protein isoform identification from expressed sequence tags and its application to peptide mass fingerprinting

Expressed Sequence Tags (ESTs) are an invaluable resource for protein ident ification and characterisation in proteomics. They allow proteins to be ide ntified in the absence of genome sequence data. When EST sequences are used for protein identification, they are usually first processed into contigs to reduce redundancy and generate longer sequences from the overlapping EST s. However, the process of generating contigs may accidentally group biolog ically meaningful isoforms together. Here we report means of discovering is oforms in EST sequences and how to use this information in the framework of protein identification and characterisation with peptide mass fingerprinti ng. We illustrate our strategies with examples from the dbEST database as w ell as protein isoforms from two-dimensional polyacrylamide gels.