Table I

Optional Boolean filters that may be used to constrain the search for MRM transitions using MRMaid

Filter criterionDescription
Peptide observation redundancyPeptide must have been seen in x% of all observations of the query protein in GAPP database
Internal cleavage sitePeptides with Lys or Arg not followed by Pro
Instrument typeConstrains to MS/MS data retrieved for the instrument setup selected
Omit Asn and GlnAsn and Gln can be deamidated resulting in m/z reproducibility issues
Peptide lengthShort 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 CysOften covalently modified, affecting m/z
Omit Gln and GluCan spontaneously cyclize to form pyroglutamate
Accept only Pro-containing peptidesProduces a very high abundance peak, suitable when a single product ion is sufficient, such as in low complexity samples
Omit Pro at any positionSelected 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