title: SWATH-based proteomics identified carbonic anhydrase 2 as a potential diagnosis biomarker for nasopharyngeal carcinoma.
abstract: Nasopharyngeal carcinoma (NPC) is a serious threat to public health, and the biomarker discovery is of urgent needs. The data-independent mode (DIA) based sequential window acquisition of all theoretical fragment-ion spectra (SWATH) mass spectrometry (MS) has been proved to be precise in protein quantitation and efficient for cancer biomarker researches. In this study, we performed the first SWATH-MS analysis comparing the NPC and normal tissues. Spike-in stable isotope labeling by amino acids in cell culture (super-SILAC) MS was used as a shotgun reference. We identified and quantified 1414 proteins across all SWATH-MS analyses. We found that SWATH-MS had a unique feature to preferentially detect proteins with smaller molecular weights than either super-SILAC MS or human proteome background. With SWATH-MS, 29 significant differentially express proteins (DEPs) were identified. Among them, carbonic anhydrase 2 (CA2) was selected for further validation per novelty, MS quality and other supporting rationale. With the tissue microarray analysis, we found that CA2 had an AUC of 0.94 in differentiating NPC from normal tissue samples. In conclusion, SWATH-MS has unique features in proteome analysis, and it leads to the identification of CA2 as a potentially new diagnostic biomarker for NPC.
authors.affiliation: Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, P. R. China.
authors.forename: Yanzhang
authors.initials: Y
authors.lastname: Luo
authors.affiliation: Department of Otorhinolaryngology, The First Affiliated Hospital, Jinan University, Guangzhou 510632, P. R. China.
authors.forename: Tin Seak
authors.initials: TS
authors.lastname: Mok
authors.affiliation: Department of Otorhinolaryngology, The First Affiliated Hospital, Jinan University, Guangzhou 510632, P. R. China.
authors.forename: Xiuxian
authors.initials: X
authors.lastname: Lin
authors.affiliation: Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, P. R. China.
authors.forename: Wanling
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, P. R. China.
authors.forename: Yizhi
authors.initials: Y
authors.lastname: Cui
authors.affiliation: Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, P. R. China.
authors.forename: Jiahui
authors.initials: J
authors.lastname: Guo
authors.affiliation: Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, P. R. China.
authors.forename: Xing
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Otorhinolaryngology, The First Affiliated Hospital, Jinan University, Guangzhou 510632, P. R. China.
authors.forename: Tao
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, P. R. China.
authors.forename: Tong
authors.initials: T
authors.lastname: Wang
mesh_terms: D014408:Biomarkers, Tumor / Q000378:metabolism*; D024402:Carbonic Anhydrase II / Q000032:analysis / Q000378:metabolism*; D002277:Carcinoma / Q000175:diagnosis* / Q000378:metabolism; D045744:Cell Line, Tumor; D006801:Humans; D013058:Mass Spectrometry; D000077274:Nasopharyngeal Carcinoma; D009303:Nasopharyngeal Neoplasms / Q000175:diagnosis* / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D012680:Sensitivity and Specificity
chemical_list: D014408:Biomarkers, Tumor; D024402:Carbonic Anhydrase II