Table II

Derivation of TS coefficients

TS is used to rank the predicted transitions in MRMaid. It is calculated as the sum of the coefficients, each relating to efficiency in MRM. Each coefficient is derived by multiplying the value by the weighting.

Transition score coefficientDescriptionRelative weighting
MS/MS suitability (q)Assesses MS/MS spectrum for suitability in MRM by assessing m/z values of y-ions50
Peptide coverage (c)Favors fragment ions that represent a greater proportion of the precursor peptide sequence8
Mass range (r)Constrains acceptable MS/MS mode mass range7
Precursor charge state (s)Doubly and triply charge peptides are favored6
Positively weighted residue content (p)His, Lys, and Arg1
Negatively weighted residue content (n)Tyr, Ser, Thr, Cys, and Met1