UniQua: A Universal Signal Processor for MS-Based Qualitative and Quantitative Proteomics Applications
Recent developments in high resolution mass spectrometry (HR-MS) technology have ushered proteomics into a new era. However, the importance of using a common, open data platform for signal processing of HR-MS spectra has not been sufficiently addressed. In this study, a MS signal processor was developed to facilitate data integration from different instruments and different proteomics approaches into a unified platform without compromising protein identification and quantitation performance. This processor supports parallel processing capability which allows full utilization of computing resources to speed up signal processing performance to >1 gigabytes/min. The storage space occupied by the processed MS data can be reduced to ∼10%, which helps the analysis and management of large quantities of data from comprehensive proteomics studies. For quantitation at the MS level, processing accuracy is improved and processing time for ASAPRatio is reduced to ∼50%. For quantitation at the MS/MS level, accurate reporter ion ratios from different instruments can be directly determined by the processed MS/MS spectra and reported in the Mascot search result directly without using specialized iTRAQ software. The software, source code, manual and raw data sets used in this study are available at http://msomics.abrc.sinica.edu.tw/UniQua/.
Yet-Ran Chen
Research Fellow
CURRENT POSITION
2024- Research Fellow, Agricultural Biotechnology Research Center, Academia Sinica.
2024- President, Taiwan Society for Mass Spectrometry.
2015- Professor, Biotechnology Center, National Chung Hsing University.
2009- Executive PI of Metabolomics Core Facility, Academia Sinica
PROFESSIONAL EXPERIENCES
2015-2024 Tenured Associate Research Fellow, Agricultural Biotechnology Research Center, Academia Sinica.
2007-2015 Assistant Research Fellow, Agricultural Biotechnology Research Center, Academia Sinica.
2006-2007 Assistant Professor, Dep. of Bioscience and Biotech., National Taiwan Ocean University.
2002-2006 Postdoctoral Research Fellow, Institute of Chemistry, Academia Sinica.
2003 Visiting Scholar, Institute for Systems Biology, Seattle, WA, USA
AWARDS
2025 Outstanding Scholar Award, Foundation for the Advancement of Outstanding Scholarship (FAOS)
2024 Investigation Research Grant/Award, Academia Sinica
2024 Distinguished Scholar Award, Taiwan Society for Mass Spectrometry
2016 Junior Research Investigators Award, National Award by Academia Sinica.
2016 Career Development Award, Academia Sinica.
2015 Professor CY Lin Memorial Award for Innovative Research Program, The Chu-Yung Lin Memorial Foundation and Taiwan Society for Plant Biologists (TSPB).
2015 The Shang-Fa Yang Young Scientist Award, The Shang-Fa Yang Memorial Foundation.
2013 TSMS Young Scholar Award, Taiwan Society for Mass Spectrometry.
2008 Biotechnology Creativity Award, Industrial Development Bureau, Ministry of Economic Affairs.
HONORS
2024- President, Taiwan Society for Mass Spectrometry.
2024 Significant Discovery, Academia Sinica 2023 Yearly Report
2021- Council Member, Taiwan Metabolomics Society.
2016 Significant Discovery, Academia Sinica 2015 Yearly Report
2015 Significant Discovery, Academia Sinica 2014 Yearly Report
2015- Council Member, Asia Oceania Agricultural Proteomics Organization.
2011- Elected Council Member / Executive Council Member (2021-), Taiwan Society for Proteomics.
2006- Elected Council Member / Chair of Publication Committee (2021-) / Executive Council Member (2015-) / Chair of Finance Committee (2015-21) / Academic Committee (2015-) / Training Course Committee (2009-12), Taiwan Society for Mass Spectrometry.