Next Generation Proteomics for Clinical Biomarker Detection Using SWATH-MS.

Abstract

The technology of "sequential windowed acquisition of all theoretical fragment ion spectra," known as SWATH-MS, is rapidly gaining popularity as a next generation proteomics technology for comprehensive proteome quantitation. In this chapter, we describe the use of SWATH-MS as a label-free quantitative technique in a proteomics study to identify novel serological biomarker for colorectal cancer. We compared the secreted glycoprotein profiles (glyco-secretomes) enriched from the colon adenocarcinoma cell line HCT-116 and its metastatic derivative, E1, and observed that laminin β-1 (LAMB1) was oversecreted in E1 cells. This novel oversecretion of LAMB1 was validated in colorectal cancer patient serum samples, and ROC analyses showed that LAMB1 performed better than carcinoembryonic antigen (CEA) as a clinical diagnostic biomarker for colorectal cancer. We focus here on the sample preparation methodology and data processing workflow for SWATH-MS studies.

• Authors: Qifeng Lin, Hwee Tong Tan, Maxey C M Chung
• Journal: Methods in molecular biology (Clifton, N.J.) (Methods Mol Biol) Vol. 1977 Pg. 3-15 ( 2019) ISSN: 1940-6029 [Electronic] United States
• PMID: 30980318 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

• Biomarkers
• Proteome

Topics

• Biomarkers
• Cell Line, Tumor
• Chromatography, Liquid
• Colorectal Neoplasms (metabolism)
• Data Analysis
• Enzyme-Linked Immunosorbent Assay
• Humans
• Proteome
• Proteomics (methods)
• ROC Curve
• Spectrum Analysis (methods)
• Tandem Mass Spectrometry
• Workflow