Supplemental Figure S1 (Adobe PDF) -
Fig. S1. GAPDH (Tdh3p and Tdh2p) is fragmented upon H2O2-induced apoptosis. For each Tdh3p (numbered 1 to 4) and Tdh2p fragment, matched peptides that were obtained after trypsin digestion and used for identification of the proteins, are shown (underlined sequence). Amino acids specific for Tdh3p and Tdh2p isoforms, are shown in red and green, respectively. Analyzing which parts of the protein sequence correspond to the spot-specific peptides in the mass spectrum can indicate putative fragmentation, since spots presenting putative fragments lack peptides observed in the mass spectrum of the whole protein. Thus, the spot position observed by 2D gel electrophoresis and the specific peptides in the corresponding mass spectrum were analyzed to define the spot as intact protein or as a protein fragment. Distinction between GAPDH isoform 2 and 3 (Tdh2p and Tdh3p) was possible because of the identification of amino acids present in the matched peptides that are specific for each GAPDH isoform.
