Optional Boolean filters that may be used to constrain the search for MRM transitions using MRMaid
| Filter criterion | Description |
|---|---|
| Peptide observation redundancy | Peptide must have been seen in x% of all observations of the query protein in GAPP database |
| Internal cleavage site | Peptides with Lys or Arg not followed by Pro |
| Instrument type | Constrains to MS/MS data retrieved for the instrument setup selected |
| Omit Asn and Gln | Asn and Gln can be deamidated resulting in m/z reproducibility issues |
| Peptide length | Short peptides (<7 or 8 amino acids) are unlikely to be unique to the target, and very long peptides will be out of mass range |
| Omit Met and Cys | Often covalently modified, affecting m/z |
| Omit Gln and Glu | Can spontaneously cyclize to form pyroglutamate |
| Accept only Pro-containing peptides | Produces a very high abundance peak, suitable when a single product ion is sufficient, such as in low complexity samples |
| Omit Pro at any position | Selected when multiple transitions per target are required, such as in high complexity samples like serum |
| Omit P1 (Pro adjacent to the C terminus) | Can produce nonspecific product y-ion |
| Omit P2 (Pro second position from C terminus) | Can produce nonspecific product y-ion |
| m/z cut off (user specifies a value, x) | Selects only fragment ion m/z >x where x is a percentage of the precursor m/z |