Best mrm candidate

The GPM's MRM database contains a listing of all of the peptide sequences and associated mass spectra associated with a particular protein sequence that may be needed to construct a multiple-reaction monitoring assay. This list is exhaustive: it contains many peptide sequences that may not be the best candidates for this type of assay. In order to simplify the task of assay development, we have developed system based on heuristics to reduce the number of candidate sequences.

Best candidate rules

The current set of heuristics for a candidate peptide sequence is as follows:

1. it must have more than 8 but fewer than 31 residues;
2. it cannot begin with Q, C, E, K, R or P;
3. it must end with K or R;
4. it cannot contain an internal H, K or R; and
5. it cannot contain the sequence "NG".

In addition, the observations must conform to the following rules:

1. the dominant observed charge state must be z=2 (ω(3) must be less than 10% of ω(2)); and
2. there cannot be observations of the same sequence extended on the N- or C-terminus by K or R.

Peptides that do not conform to these rules can be hidden or shown by clicking the link "show best candidates (*) only" on the main MRM display page for a protein.