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Supplementary Figure 1: (A) A representative example of a 1D SDS PAGE (Tris-Glycine 4–20% gradient gel) of four different serum pools with and without ProteoMinerTM workup. From left to right, protein markers (M) from 10–170 kDa, ProteoMinerTM eluates (E) from the adult control group (E1), child control group (E2), DMD ambulant group (E3) and DMD non-ambulant group (E4), and four corresponding flow through fractions. The eluate fractions were cut into ten pieces and were in-gel digested using trypsin or Lys-N. The band at 67 kDa represents albumin, which was strongly depleted in the eluates.

(B) Reproducibility of ProteoMinerTM was evaluated by loading a serum sample on four separate ProteoMinerTM columns. Eluates from the four columns are marked as 1–4.

prca1520-sup-0002-FigureS2.pdf70KSupplementary Figure 2: Peptide ID iProphet scores (1-P) plotted on a logarithmic scale.The peptide numbers in Figure 2 are based on iProphet probability values between 1 and 0.20.The lowest numbers correspond to the highest confidence levels. A = CID tryptic peptides; B = ETD tryptic peptides; C = CID Lys-N peptides; D = ETD Lys-N peptides.
prca1520-sup-0003-FigureS3.pdf34KSupplementary Figure 3: Serum fibronectin levels plotted as function of age in ambulant (crosses) and non-ambulant (circles) DMD patients.
prca1520-sup-0004-FigureS4.jpg39KSupplementary Figure 4: Serum fibronectin levels (left y-axis; blue diamonds) and CK activity measurements (right y-axis, red circles) are plotted as a function of age for the longitudinal DMD cohort.
prca1520-sup-0005-TableS1.pdf63KSupplementary Table 1: Number of peptides and proteins identified through the different digestion and fragmentation strategies.
prca1520-sup-0006-TableS2.pdf56KSupplementary Table 2: List of proteins with ≥ 2 unique peptides per protein identified (validated by ProteinProphet) from trypsin and Lys-N digestion with CID and ETD fragmentation across all four groups. The table includes protein name, molecular weight and number of spectral counts.

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