Column Match database program

Figure 3.26. Results from Column Match, a database program allowing the user to select a similar or dissimilar column to that of the specified column in the existing method.

Table 12 Identification of G3PC ARATH (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE, CYTOSOUC), Species Arabidopsis thaliana, SWISS-PROT (SP) entry P25858 using different PMF tools. The restricting parameters used were Arabidopsis thaliana for the species, a minimum number of 4 matched masses, a maximal tolerance for masses of 60 ppm, at most one missed cleavage of tryptic peptides allowed, and the modifications accepted were oxidised methionines and cysteines treated with iodoacetamide to form carboxyamidomethyl cysteines. The databases queried by each program are listed in the right column. In the score column, the first value is the score of the first candidate protein, followed by either the score of the second candidate protein (if the first one is the correct one)...

Table 13 Query for 60 mass values of a MALDI-TOF MS spectrum from a mixture of P0N2JHIUMAN (SERUM PARAOXONASE/ARYLESTERASE 2, Species Homo sapiens, SWISS-PROT accession number Q15165) and the marker GT26J5CHJA (GLUTATHIONE S-TRANSFERASE 26 KDA, Species Schistosoma japonicum, SWISS-PROT accession number P08515). The query was made for the all available species, the minimum number of matched masses was 4, the maximal tolerance for masses was 40 ppm, at most one missed cleavage for tryptic peptides was allowed, and the modifications accepted were artefactual modification of cysteines with acrylamide and oxidised methionines. Mr values were delimited between 20 and 40 kDa. The databases queried by each program are listed in the right column...

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