Supplemental Figures -
"Supplemental Figure 1. Results from searching MALDI-TOF mass spectrum data from PT24 against the Swiss Prot database. A) The sequence of RAB2A from the human; peptides matching fragments of PT24 are indicated in red and represent 48% coverage of RAB2A. B) Summary of the fragments of PT24 that matched to RAB2A. C) Histogram for mowse scores for PT24 spectra. The shaded area represents scores of less than 66 that are considered not significant. The only significant results (which received a score of 86) are members of the RAB2 subfamily.
Supplemental Figure 2. Results from searching PT24 MS/MS spectra against the Swiss Protein database. A) Sequence of human RAB2A. Where the fragments matched to PT24 the sequence is indicated in red. B) Summary of the fragments of PT24 that matched to RAB2A. Start-End indicates the position of the fragment within RAB2A. Observed indicates the mass/charge ratio observed. Mr(expt) is the observed ion mass from the MS/MS spectra. Mr(calc) is the calculated ion mass based on the sequence of RAB2A. Delta is the difference between Mr(expt) and Mr(calc). Miss is the number of missed trypsin-cleavages in the peptide. Sequence is the sequence of RAB2A corresponding to the fragment. Any modifications to these peptides are indicated in brackets.
Supplemental Figure 3. Combination of results from Q-TOF MS analysis and error tolerant searching of PT24 against human RAB2A (mouse or rabbit RAB2A gave identical results) using the Mascot search engine. While both the MALDI-TOF and Q-TOF identify the mass of peptides the Q-TOF in addition measures individual spectra generated from the collision-induced dissociation of single peptides and hence provides sequence information. A) Sequence of RAB2A from the rabbit. Fragments matched to PT24 are indicated in red and cover 72% of RAB2A. B) Error-tolerant searching, PT24 against RAB2A (Matrix Science, 2003), identified two PT24 peptides with potential single amino acid substitutions: residues 2-8 with residue 2 (alanine) of RAB2A replaced by threonine and residues 171-186 with residue 183 (asparagine) of RAB2A substituted by aspartic acid in PT24.
Supplemental Figure 4. A sample peptide view obtained from an error tolerant search of PT24 against human RAB2A (Matrix Science, 2003). The fragment matched to residues 151-176 with a substitution of N to D at residue 183. A) The MS/MS spectra obtained for the fragment. Matching fragments are indicated above their respective peaks. B) Potential collision induced dissociation fragments from RAB2A. Fragments matching the MS/MS spectra of PT24 are indicated in red.
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