Identification of the differentially expressed proteins in nasopharyngeal carcinoma by proteomics.

Background: We sought to determine the differences with respect to the proteome of nasopharyngeal tissues between patients with nasopharyngeal carcinoma (NPC) and healthy controls by using sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) and ingenuity pathway analysis (IPA). Our primary purpose was to identify specific protein markers that can be applied for diagnosis or treatment of NPC.

Methods: The CNE-1, CNE-2 and H1299 cell lines were cultured in stable isotope labeling of amino acids in cell culture (SILAC) medium for 10 generations to obtain labeled proteins.

SWATH-based proteomics identified carbonic anhydrase 2 as a potential diagnosis biomarker for nasopharyngeal carcinoma.

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.