In-depth Proteomics

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.

Integrative Multi-Omics

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.

Proteogenomics analysis

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.

Global PTM analysis to Study Signal Transduction using mass spectometry

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.