What should I be aware of when using the dbEST database?
1) Peptide mass fingerprinting in principle shouldn’t typically be very effective with ESTs because you have digested a whole protein and EST’s are only a few hundred basepairs, often on the order of 100-200. So you can only match a portion of your protein. 2) For the practical reason above the dbEST search feature was put into Protein Prospector mainly for searches using MS/MS spectra and sequence data; MS-Tag, MS-Pattern. 3) When using the web server rather than Protein Prospector on the web, you are competing for CPU time against people all over the world. So for long dbEST searches it sometimes helps to break it into 2 searches. 1 with 3 frame translation, 1 with -3.
