Browsing by Author "Ko, Chu-Ling"

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iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm
(2017-12-19)
Chang, Hui-Yin
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Chen, Ching-Tai
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Ko, Chu-Ling
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Chen, Yi-Ju
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Chen, Yu-Ju
Top-down proteomics using liquid chromatogram coupled with mass spectrometry has been increasingly applied for analyzing intact proteins to study genetic variation, alternative splicing, and post-translational modifications (PTMs) of the proteins (proteoforms). However, only a few tools have been developed for charge state deconvolution, monoisotopic/average molecular weight determination and quantitation of proteoforms from LC-MS1 spectra. Though Decon2LS and MASH Suite Pro have been available to provide intraspectrum charge state deconvolution and quantitation, manual processing is still required to quantify proteoforms across multiple MS1 spectra. An automated tool for interspectrum quantitation is a pressing need. Thus, in this paper, we present a user-friendly tool, called iTop-Q (intelligent Top-down Proteomics Quantitation), that automatically performs large-scale proteoform quantitation based on interspectrum abundance in top-down proteomics. Instead of utilizing single spectrum for proteoform quantitation, iTop-Q constructs extracted ion chromatograms (XICs) of possible proteoform peaks across adjacent MS' spectra to calculate abundances for accurate quantitation. Notably, iTop-Q is implemented with a newly proposed algorithm, called DYAMOND, using dynamic programming for charge state deconvolution. In addition, iTop-Qperforms proteoform alignment to support quantitation analysis across replicates/samples. The performance evaluations on an in-house standard data set and a public large-scale yeast lysate data set show that iTop-Q achieves highly accurate quantitation, more consistent quantitation than using intraspectrum quantitation. Furthermore, the DYAMOND algorithm is suitable for high charge state deconvolution and can distinguish shared peaks in coeluting proteoforms. iTop-Qis publicly available for download at http://ms.iis.sinica.edu.tw/COmics/Software_iTop-Q.
On solving the 7,7,5-game and the 8,8,5-game
(2020-05-02)
Hsu, Wei-Yuan
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Ko, Chu-Ling
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Chen, Jr-Chang
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Wei, Ting-Han
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Hsueh, Chu-Hsuan
An mnk-game is a kind of k-in-a-row game played on an m x nboard, where two players alternatively mark empty squares with their own colors and the first player who gets k-consecutive marks (horizontally, vertically, or diagonally) wins. In this paper, we present an AND/OR search tree algorithm specifically for proving mnk-games. We first propose three novel methods to reduce the branching factor of AND/OR search trees. We also propose a new method to find pairing strategies, which further accelerate the proof of mnk-games. The combined methods drastically speed up the proof for the 7,7,5-game, which is solved in 2.5 seconds. Moreover, this paper is the first to solve the 8,8,5-game, which is proven as a draw within 17.4 hours. (C) 2020 Elsevier B.V. All rights reserved.
Solving 7,7,5-game and 8,8,5-game
(2018-01-01)
Hsu, Wei-Yuan
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Ko, Chu-Ling
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Hsueh, Chu-Hsuan
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Wu, I-Chen
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資訊工程學系
An mnk-game is a kind of k-in-a-row game played on an m x n chess board, where two players alternatively mark empty squares with their own colors and the first one to get k-consecutive marks wins. This paper solves 7,7,5-game and 8,8,5-game as draws. In the proof, we propose some methods based on pairing strategies and potential weights, and then use a program implementing these methods to solve 7,7,5-game in about one minute and 8,8,5-game in about three days.
WinProphet: A User-Friendly Pipeline Management System for Proteomics Data Analysis Based on Trans-Proteomic Pipeline
(2019-08-06)
Chen, Ching-Tai
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Ko, Chu-Ling
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Choong, Wai-Kok
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Wang, Jen-Hung
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Hsu, Wen-Lian
Protein and peptide identification and quantitation are essential tasks in proteomics research and involve a series of steps in analyzing mass spectrometry data. Trans-Proteomic Pipeline (TPP) provides a wide range of useful tools through its web interfaces for analyses such as sequence database search, statistical validation, and quantitation. To utilize the powerful functionality of TPP without the need for manual intervention to launch each step, we developed a software tool, called WinProphet, to create and automatically execute a pipeline for proteomic analyses. It seamlessly integrates with TPP and other external command-line programs, supporting various functionalities, including database search for protein and peptide identification, spectral library construction and search, data-independent acquisition (DIA) data analysis, and isobaric labeling and label-free quantitation. WinProphet is a standalone, installation-free tool with graphical interfaces for users to configure, manage, and automatically execute pipelines. The constructed pipelines can be exported as XML files with all of the parameter settings for reusability and portability. The executable files, user manual, and sample data sets of WinProphet are freely available at http://ms.iis.sinica.edu.tw/COmics/Software_WinProphet.html.