Peptide injections

Sequence database searching is widely used currently for mass spectra based protein identification. In this approach, a protein sequence database is used to calculate all putative peptide candidates in the given setting (proteolytic enzymes, miscleavages, post-translational modifications). The sequence search engines use various heuristics to predict the fragmentation pattern of each peptide candidate. Such derivative patterns are used as templates to find a sufficiently close match within experimental mass spectra, which serves as the basis for peptide/protein identification. Many tools have been developed for this practice, which have enabled many past discoveries.

You will also notice that there are matches to peptides modified with Carbamidomethyl and Oxidation, even though no modifications were specified for the search, because these modifications were present in the library entry. Likewise, there are some matches to non-tryptic peptides (e.g. N.CLAPLAK.V) even though the enzyme in the search form was trypsin. Only a few search parameters are relevant to a library search, the most important being precursor and fragment mass tolerances.