Table I

Summary of the advantages and disadvantages with the different sequence collections

SwePep peptidesContains all known peptides, fast search, many significant hitsCannot identify novel peptides if they are not a part of an already known sequence
SwePep precursorsContains more sequences than SwePep peptides but is still fast to search and gives a good search resultOnly peptide precursors, cannot identify peptides from “novel” precursors
SwePep predictedContains all possible peptides with dibasic cleavage sites from the mouse proteome; good for identifying novel peptidesThis should only be used for identifying novel peptides because it does not contain all already known peptides
Mouse proteomeLarge sequence collection, possible to discover novel peptidesGives low number of significant peptides identities, time-consuming to search with unspecific cleavage