Abbreviation | Definition |
---|---|
DMS | Set of mass values corresponding to all possible disulfide-bonded peptide structures that can be obtained from a digested protein. |
PMS | Set of mass values of ions that undergo dissociation to produce product ions (set of precursor ions). |
IM | Correspondence obtained when the difference between the detected mass of a targeted ion from the PMS and the calculated mass of a possible disulfide-bonded peptide structure from the DMS is less than a match threshold T IM . |
T IM | Initial Match threshold. Threshold used to define a mass window centered on a PMS value within which a correspondence between a DMS value and a PMS value may be found. |
ε | DMS trimming parameter used to trim the DMS set. To trim the DMS set by ε means to remove as many elements from DMS as possible without losing meaningful mass values. |
TrimSet | Set of trimmed mass values from the DMS set. |
PM | Peptide Mass: cysteine-containing peptide mass value. |
TempSet | Temporary mass set containing possible disulfide bonded peptide structures. |
FMS | Set of mass values of every disulfide-bonded fragment structure that can be obtained from fragment ions, which can be of types a, b, bo, b*, c, x, y, yo, y*and z. |
TMS | Set of mass values of the product ions obtained after the MS/MS step (MS/MS spectra). |
VM | Correspondence obtained when the difference between a precursor ion fragment mass from TMS and a disulfide-bonded fragment structure mass from FMS falls below a validation match threshold T VM . |
T VM | Validation Match threshold. Threshold used to define a mass window centered at a TMS value in which a correspondence between a FMS value and a TMS value may be found. |
δ | FMS trimming parameter used to trim the FMS set. To trim the DMS set by δ means to remove as many elements from FMS as possible without losing meaningful fragment ions mass values. |
FragSet | Set containing the mass values of fragment ions generated by the method GENFRAGS(.) in the APROX-FMS routine. |