MS/MS Ions Search

The MS/MS ions search accepts data in the form of peak lists containing mass and intensity pairs. A single peptide may be searched, but this search mode is much more powerful when analysing an LC-MS/MS run containing data from multiple peptides. Obtaining matches to a number of peptides from a single protein provides a very high level of confidence that the result is correct.

Many of the considerations described in the description of a peptide mass fingerprint search apply equally well to an MS/MS ions search. Please refer to these notes for a discussion of choosing an enzyme, the partials parameter, and setting mass tolerances.

The high level of specificity of an MS/MS ions search means that it is not essential to choose an enzyme. However, a search in which an enzyme has been specified will be considerably faster. This is because the "no enzyme" search must test all possible subsequences of each protein, rather than just (say) tryptic peptides. For a protein of N residues, there are approximately N/10 tryptic peptides compared with N(N+1)/2 possible subsequences. For a modest size protein of 250 residues, this is an increase of three orders of magnitude in the number of peptides which must be considered.

There are two situations where the "no enzyme" search is particularly useful. The first is when the enzyme specificity is suspect. The second is when the peptides do not originate from a formal digest. An important example of this latter case is the study of MHC peptides from the immune system.