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
Associate Research Fellow
PROFESSIONAL EXPERIENCES
2015- Tenured Associate Research Fellow, Agricultural Biotechnology Research Center, Academia Sinica.
2015- Associate Professor, Department of Chemistry, National Chiayi University.
2015- Associate Professor, Institute of Biotechnology, National Taiwan University.
2015- Associate Professor, Biotechnology Center, National Chung Hsing University.
2015- Associate Professor, Institute of Bioscience and Biotechnology, National Taiwan Ocean University.
2009- Executive PI of Metabolomics Core Facility, Scientific Instrument Service Center, Academia Sinica
2010-2015 Assistant Professor, Institute of Biotechnology, National Taiwan University.
2009-2015 Assistant Professor, Biotechnology Center, National Chung Hsing University.
2007-2015 Assistant Professor, Dep. of Bioscience and Biotech., National Taiwan Ocean University.
2007-2015 Assistant Research Fellow, Agricultural Biotechnology Research Center, Academia Sinica.
2002-2006 Postdoctoral Research Fellow, Institute of Chemistry, Academia Sinica.
2003 Visiting Scholar, Institute for Systems Biology, Seattle, WA, USA
AWARDS
2016 Junior Research Investigators Award, Academia Sinica.
2016 Career Development Award, Academia Sinica.
2015 Professor CY Lin Memorial Award for Innovative Research Program
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
2015- Council Member, Asia Oceania Agricultural Proteomics Organization.
2015- Executive Council Member, Taiwan Society for Mass Spectrometry
2012-2015 Chair of Finance Committee/Academic Committee, Taiwan Society for Mass Spectrometry
2015- Elected Council Member, Taiwan Society for Mass Spectrometry
2014- Elected Council Member, Taiwan Society for Proteomics
2012-2015 Chair of Finance Committee/Training Course Committee, Taiwan Society for Mass Spectrometry
2012-2015 Elected Council Member, Taiwan Society for Mass Spectrometry
2011-2014 Elected Council Member, Taiwan Society for Proteomics
2009-2012 Elected Council Member/Training Course Committee, Taiwan Society for Mass Spectrometry
2006-2009 Elected Council Member, Taiwan Society for Mass Spectrometry