Advance in mass spectrometry has enabled researchers to explore a proteome in a day very rapidly. Nonetheless, in-depth proteome analysis in a given time is still challenging due to the complexity of the proteome. I have contributed to optimizing methodologies to increase the rate of protein identifications. For example, I systematically assessed impacts of parameters on protein/peptide identification. In addition, I have proved that alternative fragmentation method by combining CID to ETD improves site localization of phosphorylation.
Recent advance in multi-omics technologies allows researchers to study a system thoroughly. Since we are interested in understanding the biological system comprehensively, we employ these techniques to collect data sets on the multi-layers.
Mass spectrometry combined to bioinformatic methods is a promising technology to identify novel genomic regions that are yet to be annotated as coding. Using this approach, I have contributed to identify hundreds of novel protein-coding genes. Some of them were annotated as non-coding RNAs while others were thought to be not expressed to function (e.g. pseudogenes). Multi-Omic analysis method by combining transcriptome to proteome of a single donor has proven its uniqueness to annotate the current human genome.
Mass spectrometry became an essential tool to study post-translational modifications in a high-throughput fashion. I have constantly sought to establish analytical workflows to study these modifications using mass spectrometry. For example, I have used TiO2 and IMAC to enrich abundant phosphorylation in an unbiased manner as well as anti-tyrosine phosphorylation antibodies to enrich low abundant tyrosine phosphorylation. In addition, I have established antibody-based enrichment for ubuiquitination.
Signal transduction is a pivotal mechanism underlying uncontrolled growth of cancer cells as well as controlled normal cell growth and differentiation. Mass spectrometry is a tool to study proteins and its modifications providing the large-scale knowledge about them. My study on tyrosine phosphorylation in pancreatic cancer have revealed heterogeneity and demonstrated personalized therapy by helping select those patients.