Institute of Information Science, Academia Sinica

Genomics, transcriptomics, proteomics, and metabolomics can be applied in biomarker identification as sources of candidate biomarkers and are studied by different experiment technologies. Liquid chromatography (LC) combined with mass spectrometry (MS) has become a predominant technology for proteomics research and been rising to be a promising technology for metabolomics. In this talk, we will focus on MS-based proteomics and briefly introduce MS-based metabolomics.

 

Biological samples, e.g., peptides or metabolites, will be separated by LC and then processed by tandem MS. The generated MS spectra and MS/MS spectra are analyzed to determine the identities and quantities of biological samples. In terms of MS-based proteomics, the key tasks of bioinformatics analyses are protein identification and quantitation. In the past, we have developed a suite of protein quantitation tools that are comprehensive for various quantitation experiment techniques. Regarding protein identification, the most successful and widely approach is sequence database searching.However, sequence database searching now encounters a bottleneck in analysis of large and sophisticated proteomics data (especially on modified proteins) due to complication of fragmentation patterns, low-abundance of modified proteins in the sample, unknown mass shifts of modifications. We will present challenges and opportunities for protein identification. Bioinformatics for metabolomics research, particularly on metabolite identification, is in primitive stage. We will briefly describe the current status and opportunities.