Research Fellow  |  Sung, Ting-Yi  
Software Name:iScore: an automated tool for phosphorylation site assignment
Inventors:Ting-Yi Sung, Wen-Lian Hsu, Sheng-Jay Lu, Lien-Chin Chen, Chih-Chiang Tsou, and in collaboration with Dr. Yu-Ju Chen
Software Name:IDEAL-Q: An Automated Tool for High-Performance label-free quantitation with an efficient elution time prediction algorithm
Inventors:Ting-Yi Sung, Wen-Lian Hsu, Chih-Chiang Tsou, Ethan Yin-Hao Tsui, Ke-Shiuan Lynn, and in collaboration with Dr. Yu-Ju Chen
Abstract:IDEAL-Q is an automated analysis tool for label-free quantitative proteomics. It accepts generic input format including mzXML raw data format and Mascot, SEQUEST, PeptideProphet/ProteinProphet for search result. IDEAL-Q uses an algorithm, called IDEAL (ID-based Elution time prediction by frAgmentaL regression), to predict the elution time based on confident peptide identification (ID) result, and thus the predicted elution time together with precursor m/z to can be used to locate the peptide signal in other LC-MS runs. In comparison with conventional identity-based label-free quantitation analysis, the quantitation coverage in terms of percentage of identified peptides and proteins can be much increased. Furthermore, the tool adopts an stringent validation stelp on Signal-to-noise ratio, Charge state, Isotopic distribution (SCI validation) and modification type using computational and statistical methods so that quantitation accuracy can be ensured even with increased quantitation coverage. IDEAL-Q provides variously optional normalization tools for flexible workflow design such as addition of fractionation strategies and multiple spiked internal standards. Furthermore, many user-friendly interfaces and statistical charts are provided in IDEAL-Q for user to conveniently inspect and validate the quantitation result and also enable to manually re-quantify data. It also provides comprehensible output reports in various formats with useful visualization diagrams and statistical analysis. IDEAL-Q can be downloaded from
Software Name:Multi-Q: a fully automated tool for multiplexed protein quantitation
Inventors:Ting-Yi Sung, Wen-Lian Hsu, Wei-Neng Hung, Wen-Ting Lin, Yi-Hwa Yian, Kun-Pin Wu, Paul CY Yu, Ethan Tsui and in collaboration with Dr. Yu-Ju Chen
Abstract:Multi-Q is developed for multiplexed iTRAQ-based quantitation in protein profiling. It is designed as a generic platform that can accommodate various input data formats from search engines and mass spectrometer manufacturers. To calculate peptide ratios, the software automatically processes iTRAQ’s signature peaks, including peak detection, background subtraction, isotope correction, and normalization to remove systematic errors. Furthermore, Multi-Q allows users to define their own data-filtering thresholds based on semi-empirical values or statistical models so that the computed results of fold changes in peptide ratios are statistically significant. This feature facilitates the use of Multi-Q with various instrument types with different dynamic ranges, which is an important aspect of iTRAQ analysis. Multi-Q is executable on the Windows Platform and available for download at
Software Name:MaXIC-Q: A Fully Automated Generic Tool Using Statistical and Computational Methods for Protein Quantitation Based on Stable Isotope Labeling and LC-MS
Inventors:Ting-Yi Sung, Wen-Lian Hsu, Ethan Yin-Hao Tsui, Yi-Hwa Yian, Chih-Chiang Tsou, Paul Chuan-Yih Yu and in collaboration with Dr. Yu-Ju Chen
Abstract:MaXIC-Q is designed as a generic tool for quantitation using differential isotope-labeling techniques, e.g., SILAC, ICAT, ICPL labelings, and user-developed labeling methods. The tool can also accommodate search results from SEQUEST and Mascot, as well as mzXML files converted from raw files produced by various mass spectrometers. MaXIC-Q contains a filtering module that allows users to filter out low-confidence search results. Statistical and computational methods are applied to construct two kinds of elution profiles for each ion, namely, PIMS (projected ion mass spectrum) and XIC (extracted ion chromatogram); the latter is used to quantify the ion ratio. To ensure that the data used for quantitation analysis is of high quality, MaXIC-Q defines validation criteria for PIMSs so that ions interfered with by co-eluting peptides or noise can be detected. MaXIC-Q can be downloaded from
Software Name:Bioinformatics online web services
Inventors:Wen-Lian Hsu, Ting-Yi Sung, Hua-Sheng Chiu, Allan Lo, Jia-Ming Chang, Chia-Yu Su, Yi-Wen Yang, Chin-Tai Chen, Hsin-Nan Lin, Yi-Yuan Chiu
Abstract:Please visit the webpage of the IASL Lab at