Comparative proteomics, network analysis and post-translational modification identification reveal differential profiles of plasma Con A-bound glycoprotein biomarkers in gastric cancer Yih-Huei Uen a, b, c , d, 1 , Kai-Yuan Lin c , e , 1 , Ding-Ping Sun b, 1 , Chen-Chung Liao f , 1 , Ming-Song Hsieh g, h, i , Yung-Kai Huang j , Yen-Wei Chen k , Pei-Hsuan Huang f , Wei-Jung Chen l , Chih-Chun Tai m , Kuan-Wei Lee i , You-Chia Chen i , Ching-Yu Lin i , ⁎ a Superintendent's Office, Chi-Mei Hospital Chiali, Tainan 722, Taiwan b Division of General Surgery, Department of Surgery, Chi-Mei Medical Center, Tainan, 710, Taiwan c Department of Medical Research, Chi-Mei Medical Center, Tainan 710, Taiwan d Institute of Biomedical Engineering, Southern Taiwan University of Science and Technology, Tainan 710, Taiwan e Department of Biotechnology, Chia Nan University of Pharmacy and Science, Tainan 717, Taiwan f Proteomics Research Center, National Yang-Ming University, Taipei, Taiwan g Department of Infection Control, Microbiological Laboratory, Taipei Medical University-Shuang-Ho Hospital, Taipei Medical University, New Taipei City, Taiwan h Department of Medical Laboratory Science and Biotechnology, Central Taiwan University, Taichung, Taiwan i School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan j School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taiwan k Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu 30013, Taiwan l Institute of Biotechnology, National Ilan University, Ilan 26047, Taiwan m Department of Laboratory Medicine, Taipei Medical University-Shuang-Ho Hospital, Taipei Medical University, New Taipei City, Taiwan ARTICLE INFO ABSTRACT Article history: Received 11 May 2012 Accepted 10 March 2013 In the study, we used Con A affinity chromatography, 1-D gel electrophoresis, and nano-LC–MS/MS to screen biomarker candidates in plasma samples obtained from 30 patients with gastric cancer and 30 healthy volunteers. First, we pooled plasma samples matched by age and sex. We identified 17 differentially expressed Con A-bound glycoproteins, including 10 upregulated proteins and 7 downregulated proteins; these differences were significant (Student's t-test, p-value < 0.05). Furthermore, 2 of the upregulated proteins displayed expression levels that were increased by 2-fold or more in gastric cancer samples when compared with normal control samples. These proteins included leucine-rich alpha-2-glycoprotein (LRG1) and inter- alpha-trypsin inhibitor heavy chain H3 (ITIH3), and the expression levels were validated by Western blot analysis. Pathway and network analysis of the differentially expressed proteins by Ingenuity Pathway Analysis revealed vital canonical pathways involving acute phase response signaling, the complement system, LXR/RXR activation, hematopoiesis from pluripotent Keywords: Gastric cancer Glycoproteins Concanavalin A Mass spectrometry Post-translational modification Human plasma JOURNAL OF PROTEOMICS 83 (2013) 197 – 213 ⁎ Corresponding author at: School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, No. 250, Wuxing Street, Taipei 11031, Taiwan. Tel.: +886 2 2736 1661x3326; fax: +886 2 27324510. E-mail address: cylin@tmu.edu.tw (C.-Y. Lin). 1 Equal contribution. 1874-3919/$ – see front matter © 2013 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.jprot.2013.03.007 Available online at www.sciencedirect.com www.elsevier.com/locate/jprot