Biomarker Discovery and Verification of Esophageal Squamous Cell Carcinoma Using Integration of SWATH/MRM

We propose an efficient integration
of SWATH with MRM for biomarker
discovery and verification when the corresponding ion library is well
established. We strictly controlled the false positive rate associated
with SWATH MS signals and carefully selected the target peptides coupled
with SWATH and MRM. We collected 10 samples of esophageal squamous
cell carcinoma (ESCC) tissues paired with tumors and adjacent regions
and quantified 1758 unique proteins with FDR 1% at protein level using
SWATH, in which 467 proteins were abundance-dependent with ESCC. After
carefully evaluating the SWATH MS signals of the up-regulated proteins,
we selected 120 proteins for MRM verification. MRM analysis of the
pooled and individual esophageal tissues resulted in 116 proteins
that exhibited similar abundance response modes to ESCC that were
acquired with SWATH. Because the ESCC-related proteins consisted of
a high percentile of secreted proteins, we conducted the MRM assay
on patient sera that were collected from pre- and postoperation. Of
the 116 target proteins, 42 were identified in the ESCC sera, including
11 with lowered abundances postoperation. Coupling SWATH and MRM is
thus feasible and efficient for the discovery and verification of
cancer-related protein biomarkers.