Next Generation Proteomics for Clinical Biomarker Detection Using SWATH-MS

  • Qifeng Lin
  • Hwee Tong Tan
  • Maxey C. M. ChungEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1977)


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.

Key words

Data-independent acquisition SWATH-MS Colorectal cancer Secretome Biomarker 



Q.L. acknowledges the support of a National University of Singapore research scholarship. The authors also acknowledge the funding from the National Medical Research Council, Singapore (NMRC grant 1217/2009).


  1. 1.
    Gillet LC, Navarro P, Tate S et al (2012) Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics 11(6):O111.016717CrossRefGoogle Scholar
  2. 2.
    Liu Y, Huttenhain R, Surinova S et al (2013) Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS. Proteomics 13(8):1247–1256CrossRefGoogle Scholar
  3. 3.
    Lin Q, Lim HS, Lin HL et al (2015) Analysis of colorectal cancer glyco-secretome identifies laminin beta-1 (LAMB1) as a potential serological biomarker for colorectal cancer. Proteomics 15(22):3905–3920CrossRefGoogle Scholar
  4. 4.
    Bray F, Ren JS, Masuyer E, Ferlay J (2013) Global estimates of cancer prevalence for 27 sites in the adult population in 2008. Int J Cancer 132(5):1133–1145CrossRefGoogle Scholar
  5. 5.
    Jemal A, Bray F, Center MM et al (2011) Global cancer statistics. CA Cancer J Clin 61(2):69–90CrossRefGoogle Scholar
  6. 6.
    van der Schouw YT, Verbeek AL, Wobbes T et al (1992) Comparison of four serum tumour markers in the diagnosis of colorectal carcinoma. Br J Cancer 66(1):148–154CrossRefGoogle Scholar
  7. 7.
    Carpelan-Holmstrom M, Haglund C, Lundin J et al (1996) Pre-operative serum levels of CA 242 and CEA predict outcome in colorectal cancer. Eur J Cancer 32A(7):1156–1161CrossRefGoogle Scholar
  8. 8.
    Carriquiry LA, Pineyro A (1999) Should carcinoembryonic antigen be used in the management of patients with colorectal cancer? Dis Colon Rectum 42(7):921–929CrossRefGoogle Scholar
  9. 9.
    Harrison LE, Guillem JG, Paty P, Cohen AM (1997) Preoperative carcinoembryonic antigen predicts outcomes in node-negative colon cancer patients: a multivariate analysis of 572 patients. J Am Coll Surg 185(1):55–59CrossRefGoogle Scholar
  10. 10.
    Moertel CG, O'Fallon JR, Go VL et al (1986) The preoperative carcinoembryonic antigen test in the diagnosis, staging, and prognosis of colorectal cancer. Cancer 58(3):603–610CrossRefGoogle Scholar
  11. 11.
    Chiu KH, Chang YH, Liao PC (2013) Secretome analysis using a hollow fiber culture system for cancer biomarker discovery. Biochim Biophys Acta 1834(11):2285–2292CrossRefGoogle Scholar
  12. 12.
    Wu HY, Chang YH, Chang YC, Liao PC (2009) Proteomics analysis of nasopharyngeal carcinoma cell secretome using a hollow fiber culture system and mass spectrometry. J Proteome Res 8(1):380–389CrossRefGoogle Scholar
  13. 13.
    Yang Z, Hancock WS (2004) Approach to the comprehensive analysis of glycoproteins isolated from human serum using a multi-lectin affinity column. J Chromatogr A 1053(1–2):79–88CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Qifeng Lin
    • 1
  • Hwee Tong Tan
    • 1
  • Maxey C. M. Chung
    • 1
    Email author
  1. 1.Department of Biochemistry, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore

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