Name of platform: MS-based Multi-Omics Platform

Person in Charge: Ying-Lan Chen

1. Motive for Establishment:

 Mass spectrometry-based multi-omics technology allows for rapid and sensitive identification and quantitative analysis of a large number of proteins and small molecules in order to elucidate the differential expression and various modifications of these molecules in different biological states. This enables researchers to gain insights into the physiological changes within cells and explore key regulatory factors. As sequencing technologies have become more comprehensive, and an increasing number of biological genomes have been sequenced, proteomics and metabolomics have now become one of the most critical subjects in the post-genomic era for life sciences and biomedical fields. Due to the lack of an established core facility dedicated to mass spectrometry-based multi-omics analysis methods at our university and considering the high demand for such research internally, coupled with the limited services available from external units unable to meet our institution’s extensive needs, we have established the MS-based Multi-Omics Platform within the Center for Bioscience and Biotechnology.

2. Goals of Establishment:

 The establishment of this core facility’s goal is to create a technical platform for multi-omics research, utilizing various types of mass spectrometry core technologies. It is anticipated to encompass applications in proteomics, peptidomics, metabolomics, and other omics disciplines. The facility is planned to begin providing analysis services by the end of 2024. This facility will provide professional technical services through an open and shared experimental platform. It will regularly host educational training sessions on sample preparation and multi-omics big data analysis for mass spectrometry-based multi-omics research. Our commitment lies in enhancing the quality of teaching and research in our institution’s specialized fields.

3. Technical Service Items:

1. Metabolomics-related Services:

1. Targeted metabolite analysis (amino acids, short-chain fatty acids, TCA cycle, disease-related biomarkers).
2. Untargeted profiling metabolomics analysis(ploar and non-polar metabolomics analysis, lipidomics). 

2. Proteomics-related Services:

1. Protein identification.
2. Post-translational modification identification of proteins.
3. Data-dependent or data-independent proteome quantitative analysis.
4. Phosphoproteomics.
5. Targeted peptide quantitative analysis.

3. Software Analysis Services:

1. Protein database search and comparison.
2. Analysis of protein expression level differences.
3. Metabolite database search and comparison.
4. Analysis of metabolite expression level differences.

4. Core Facility Management:

1. Establishment of core facility research and the Technical Development Committee.
   1. Establishment of core facility basic technical service items.
   2. Establishment of core facility featured technical items.
   3. Formulation of core facility research and development directions.
   4. Provision of educational training courses and sharing platforms.
2. Establishment of the Core Facility Management and Supervisory Committee.

1. Formulation of core facility service regulations and fee standards.
2. Evaluation of core facility management and technicians’ performance.
3. User satisfaction surveys and assessments for service quality.