Protein expression in GISTs from patients treated with imatinib mesylate. A) SDS-PAGE (4-12% bis-Tris gel) of total protein extracts from three highly responsive GIST patients (lanes C-E) and from one poorly responsive patient with stable disease (lane B). A tumor tissue sample from an untreated GIST patient is shown as the control (lane A). A pool of plasma samples from healthy subjects (lane F) is shown for comparison with GIST extracts. Lanes G and H demonstrate the protein coverage of SCGF isoforms assessed by MALDI-TOF-MS of tryptic peptides obtained from digestion of the proteins in bands 8 and 9, respectively. The boxed sequences correspond to the sequence without signal peptide (amino acids 1-21) of SCGF-α (Q9Y240) that is available in the Aldente (ExPASy Proteomics Server) database. Capital letters indicate the sequence detected by MS, while the underlined sequence indicates the 78 amino acids that are lacking in the β-form. Bold numbers denote the proteins identified by MS and listed in panel B. B) Proteins identified in GIST 5 (lane E) after SDS-PAGE fractionation, tryptic digest, and MALDI-TOF-MS. 1Number refers to the specific band position on the SDS-PAGE in Figure 1A, lane E. 2Swiss-Prot/TrEMBL accession line. 3Swiss-Prot/TrEMBL description line. 4Theoretical protein mass.