Multiplex targeted proteomic assay for biomarker detection in plasma: a pancreatic cancer biomarker case study.
Biomarkers are most frequently proteins that are measured in the blood. Their development largely relies on antibody creation to test the protein candidate performance in blood samples of diseased versus nondiseased patients. The creation of such antibody assays has been a bottleneck in biomarker progress due to the cost, extensive time, and effort required to complete the task. Targeted proteomics is an emerging technology that is playing an increasingly important role to facilitate disease biomarker development. In this study, we applied a SRM-based targeted proteomics platform to directly detect candidate biomarker proteins in plasma to evaluate their clinical utility for pancreatic cancer detection. The characterization of these protein candidates used a clinically well-characterized cohort that included plasma samples from patients with pancreatic cancer, chronic pancreatitis, and healthy age-matched controls. Three of the five candidate proteins, including gelsolin, lumican, and tissue inhibitor of metalloproteinase 1, demonstrated an AUC value greater than 0.75 in distinguishing pancreatic cancer from the controls. In addition, we provide an analysis of the reproducibility, accuracy, and robustness of the SRM-based proteomics platform. This information addresses important technical issues that could aid in the adoption of the targeted proteomics platform for practical clinical utility.
Department of Medicine, University of Washington , Seattle, Washington 98195, United States. shengp@medicine.washington.edu
Sheng
S
Pan
Ru
R
Chen
Randall E
RE
Brand
Sarah
S
Hawley
Yasuko
Y
Tamura
Philip R
PR
Gafken
Brian P
BP
Milless
David R
DR
Goodlett
John
J
Rush
Teresa A
TA
Brentnall
D048948:14-3-3 Proteins / Q000097:blood / Q000737:chemistry; D000595:Amino Acid Sequence; D019540:Area Under Curve; D014408:Biomarkers, Tumor / Q000097:blood* / Q000737:chemistry; D021441:Carcinoma, Pancreatic Ductal / Q000097:blood*; D016022:Case-Control Studies; D011508:Chondroitin Sulfate Proteoglycans / Q000097:blood / Q000737:chemistry; D004797:Enzyme-Linked Immunosorbent Assay; D005092:Exonucleases / Q000097:blood / Q000737:chemistry; D005095:Exoribonucleases; D018260:Gelsolin / Q000097:blood / Q000737:chemistry; D006801:Humans; D007632:Keratan Sulfate / Q000097:blood / Q000737:chemistry; D000071234:Lumican; D008969:Molecular Sequence Data; D010190:Pancreatic Neoplasms / Q000097:blood*; D010446:Peptide Fragments / Q000737:chemistry; D010449:Peptide Mapping; D010865:Pilot Projects; D040901:Proteomics; D012372:ROC Curve; D019715:Tissue Inhibitor of Metalloproteinase-1 / Q000097:blood / Q000737:chemistry
D048948:14-3-3 Proteins; D014408:Biomarkers, Tumor; D011508:Chondroitin Sulfate Proteoglycans; D018260:Gelsolin; C000604306:LUM protein, human; D000071234:Lumican; D010446:Peptide Fragments; C560822:TIMP1 protein, human; D019715:Tissue Inhibitor of Metalloproteinase-1; D007632:Keratan Sulfate; D005092:Exonucleases; D005095:Exoribonucleases; C413442:SFN protein, human