title: Biomarker Discovery and Verification of Esophageal Squamous Cell Carcinoma Using Integration of SWATH/MRM.
abstract: 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.
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101, China.|University of Chinese Academy of Sciences , Beijing 100049, China.|Proteomics Division, BGI-Shenzhen , Shenzhen, Guangdong 518083, China.
authors.forename: Guixue
authors.initials: G
authors.lastname: Hou
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101, China.
authors.forename: Xiaomin
authors.initials: X
authors.lastname: Lou
authors.affiliation: National Laboratory of Molecular Oncology, Cancer Institute & Hospital, Chinese Academy of Medical Sciences , 17 Panjiayuan, Chaoyangqu, Beijing 100021, China.
authors.forename: Yulin
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Proteomics Division, BGI-Shenzhen , Shenzhen, Guangdong 518083, China.
authors.forename: Shaohang
authors.initials: S
authors.lastname: Xu
authors.affiliation: Proteomics Division, BGI-Shenzhen , Shenzhen, Guangdong 518083, China.
authors.forename: Jin
authors.initials: J
authors.lastname: Zi
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101, China.|Proteomics Division, BGI-Shenzhen , Shenzhen, Guangdong 518083, China.
authors.forename: Quanhui
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Proteomics Division, BGI-Shenzhen , Shenzhen, Guangdong 518083, China.
authors.forename: Baojin
authors.initials: B
authors.lastname: Zhou
authors.affiliation: National Laboratory of Molecular Oncology, Cancer Institute & Hospital, Chinese Academy of Medical Sciences , 17 Panjiayuan, Chaoyangqu, Beijing 100021, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Han
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Wu
authors.affiliation: National Laboratory of Molecular Oncology, Cancer Institute & Hospital, Chinese Academy of Medical Sciences , 17 Panjiayuan, Chaoyangqu, Beijing 100021, China.
authors.forename: Xiaohang
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Proteomics Division, BGI-Shenzhen , Shenzhen, Guangdong 518083, China.
authors.forename: Liang
authors.initials: L
authors.lastname: Lin
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101, China.|Proteomics Division, BGI-Shenzhen , Shenzhen, Guangdong 518083, China.
authors.forename: Siqi
authors.initials: S
authors.lastname: Liu
mesh_terms: D014408:Biomarkers, Tumor / Q000378:metabolism*; D002294:Carcinoma, Squamous Cell / Q000378:metabolism*; D004938:Esophageal Neoplasms / Q000378:metabolism*; D006801:Humans; D009363:Neoplasm Proteins / Q000378:metabolism; D040901:Proteomics
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins
keywords: ESCC; MRM; SWATH; biomarker