. Author manuscript; available in PMC: 2011 Nov 15.

Published in final edited form as: J Proteome Res. 2010 Aug 6;9(8):4053–4060. doi: 10.1021/pr1002559

Table 1.

Pseudo code for searching disulfide(s) within the UStag-specified proteins with anchor sequences.


FUNCTION FindDisulfides (Pept, Prot, dM, Prec)

        CONST dMCys := −1.007825 – mass modification on Cys-residue

Input

        Pept – anchor peptide sequence (contains at least 1 Cys)
        Prot - protein sequence containing Pept
        dM – mass difference to explain (k * dMCys: k=1,2,3,…)
        Prec – mass precision in amu (0.005)

Output

        Disulfides – array of disulfides explaining dM in Pept-Prot
context

Main Loop

        cntC – count of Cys residues in prefix and suffix part of Pept
        Pept1 – Prot predicted peptide linked to Pept via disulfide bond
        Pept1M – expected mass of Pept1
        IF (cntC MOD 2 = 0) THEN
           FOR i := 1 TO cntC \ 2
               IF Abs(dM − i * 2 * dMCys) < Prec THEN
                  [Pept & “d-bond” & i] -> Disulfides
               END IF
           END FOR
        ELSE
           CPos := Find 1st Cys in (Prot-Pept); −1 if not found
           DO WHILE CPos > 0
               Pept1M := dM – dMCys
               i := 0
               DO WHILE Pept1M > (dM – (cntC – 1) * dMCys - Prec)
                   GENERATE all sequences Seq around CPos such that
                             Abs(Pept1M – SeqM) < Prec
                   IF i > 0 THEN
                     [[Pept & “d-bond” & i] & “d-bond” & Seq] ->
Disulfides
                   ELSE
                       [Pept & “d-bond” & Seq] -> Disulfides
                   END IF
                   Pept1M := dM – 2 * dMCys
                   i := i −1
               LOOP
               CPos := Find next Cys in (Prot-Pept); −1 if not found
           LOOP
        END IF
        RETURN Disulfides