Distinguished Research Fellow/Professor  |  Hsu, Wen-Lian  
Personal (New window)
lab (New window)
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
  1.  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: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

 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 Services
Inventors:Hsu, Wen-Lian
Abstract:Please visit the IASL Lab webpage:
Software Name:Bioinformatics online web services
Inventors:Wen- Lian Hsu, Ting-Yi Sung, Hua-Sheng Chiu, Allan Lo, Jia-Ming

Please visit the webpage of the IASL Lab at

Software Name:Going Input Method(I)(going)
Inventors:Hsu, Wen-Lian
Abstract:Going Chinese input method is developed under cooperation between IQ-T and the Institute of Information, Academia Sinica in Taiwan. It relies on the tremendous semantic rules of the input content. Therefore, it enable users type the correct words at the first time without time-consuming job of selection. While typing, it can fix the possible typing mistakes automatically. Going input method has not only applied to phonetic Bopomofo input, but also to Cangjie input method (倉頡輸入法)and Dayi method.(大易輸入法) It won the prize of top ten most distinguished Chinese computer products in 1993. The practical edition of Going input method had been approved by the Ministry of Education as administrative usage of every educational institute. It has been downloaded over 1 million times since 1999.
Software Name:Polaris Financial Group Intelligent QA system
Inventors:Hsu, Wen-Lian
Abstract:Polaris Financial Group Intelligent QA system has been served online as customer service system since 1st March, 2000.
Software Name:Sinica QA system
Inventors:Hsu, Wen-Lian
Abstract:Sinica QA system provides various living information and important announcements of Academia Sinica. Website:
Software Name:HINET104 directory service system
Inventors:Hsu, Wen-Lian
Abstract:HINET104 directory service is online on 15th July 1998. It applies semantic filtering function to the search engine and serves as online assistance to Chunghwa Telecom.
Software Name:Going Input Method(II)(Open Chinese)
Inventors:Hsu, Wen-Lian
Abstract:GOING Chinese IME "GOING Chinese IME (also called Natural Chinese Input)" was originated from "Going Input" which was developed in 1990 by Dr. Wen-Lian Hsu of Acadamia Sinica of Taiwan, and is a Chinese input software built-in with artificial intelligence and rich Chinese semantic and lexicon database. After more than 10 years improvement, GOING Chinese IME has become a very popular and powerful Chinese input software in Taiwan and adopted by about 1.5 million users. It has always been the most popular commercial Chinese input product.   Having large amount of Chinese semantic and lexicon databases, GOING Chinese IME has gradually become a very important platform for learning and teaching Chinese. Students, teachers, the parents of children, compatriots living abroad, even foreigners choose GOING Chinese IME to learning Traditional Chinese. Allowing users to type Simplified Chinese in Traditional Chinese environment and Traditional Chinese in Simplified one, this input software is common used by alien workers, international companies, and various online surfers who often need to communicate with net friends from China. For the convenience of the old and disadvantaged people, "Magnified Input Window", "Real-time Voice Reading", and "Braille Output", "Chinese Input Method Editor with Auto Correction" functions, Chinese text input is much more efficient and output text is much more readable and the most important contribution is this software successfully assist visually impaired individuals, individuals with learning disabilities, ALS patients and any other handicapped individuals to overcome the obstacles on Chinese text input. The latest version is version 8 which released on April 28, 2005 and this project is ongoing.