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Table 1 Abbreviations and their definitions

From: An efficient algorithmic approach for mass spectrometry-based disulfide connectivity determination using multi-ion analysis

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.