Identification of glycoproteins as candidate biomarkers for nasopharyngeal carcinoma using Fe3O4@PDA@MOF-IDA and mM-TiO2@Cys enrichment and HPLC-MS proteomic analysis.

Protein biomarkers have great significance for the early diagnosis of diseases. However, the discovery and validation of novel biomarkers in mass spectrometry-based proteomics remain challenging due to the inherently low abundance of glycoproteins and the presence of interfering substances. Efficient glycopeptide enrichment strategies enable the identification of glycoproteins from complex biological samples, thereby laying the foundation for biomarker discovery. This research proposed concise pre-treatment and two types of associated data processing methods for identifying potential protein biomarkers, leveraging glycopeptide enrichment using nanomaterials with different enrichment specificities obtained through diverse material design strategies. As the foundation for implementing this method, the microporous structured nanomaterial Fe3O4@PDA@MOF-IDA and the mesoporous structured nanomaterial mM-TiO2@Cys are synthesized to acquire comprehensive protein information with varying orientation. The synthesized nanomaterials both demonstrate excellent enriching performances, including a high enrichment capacity, a spectacular selectivity, and an excellent spatial confinement ability. After the acquired raw data were subjected to database searches using two software platforms, relevant protein information was obtained. By applying two data processing methods to analyze the search results from the two software platforms, respectively, 2 glycoproteins were successfully identified as novel potential quality-expressed proteins for nasopharyngeal carcinoma.