| Issue Date | Title | Author(s) | Relation | scopus | WOS | Fulltext/Archive link |
| 2021 | A data-independent acquisition-based global phosphoproteomics system enables deep profiling | Kitata, Reta Birhanu; Choong, Wai-Kok; Tsai, Chia-Feng; Lin, Pei-Yi; Chen, Bo-Shiun; Chang, Yun-Chien; Nesvizhskii, Alexey I.; Sung, Ting-Yi; Chen, Yu-Ju | Nature Communications 12, 2539 | | | |
| 2009 | A Simple Label-free LC-MS/MS Strategy Towards Comprehensive Phosphoproteomics View that Depict the Mechanisms of Cancer Cell Invasion | Wang, Yi-Ting; Tsai, Chia-feng; Hong, Tzu-Chan; Tsou, Chih-Chiang; Lin, Pei-Yi; Hong, Tse-Ming; Yang, Pan-Chyr; Sung, Ting-Yi; Hsu, Wen-Lian; Chen, Yu-Ju | | | | |
| 2023 | A Suspension Trapping–Based Sample Preparation Workflow for Sensitive Plant Phosphoproteomics | Chen, Chin-Wen; Tsai, Chia-Feng; Lin, Miao-Hsia; Lin, Shu-Yu ; Hsu, Chuan-Chih | bioRxiv | | | |
| 2011 | An Informatics-assisted Label-free Approach for Personalized Tissue Membrane Proteomics: Case Study on Colorectal Cancer | Han, Chia-Li; Chen, Jinn-Shiun; Chan, Err-Cheng; Wu, Chien-Peng; Yu, Kun-Hsing; Chen, Kuei-Tien; Tsou, Chih-Chiang; Tsai, Chia-Feng; Chien, Chih-Wei; Kuo, Yung-Bin; Lin, Pei-Yi; Yu, Jau-Song; Hsueh, Chuen; Chen, Min-Chi; Chan, Chung-Chuan; Chang, Yu-Sun; Chen, Yu-Ju | MOLECULAR & CELLULAR PROTEOMICS 10,1-15 | | | |
| 2010 | An informatics-assisted label-free quantitation strategy that depicts phosphoproteomic profiles in lung cancer cell invasion | Wang, Yi-Ting; Tsai, Chia-Feng; Hong, Tzu-Chan; Tsou, Chih-Chiang; Lin, Pei-Yi; Pan, Sih-Hua; Hong, Tse-Ming; Yang, Pan-Chyr; Sung, Ting-Yi; Hsu, Wen-Lian; Chen, Yu-Ju | | | | |
| 2010 | An Informatics-assisted Label-free Quantitation Strategy that Depicts Phosphoproteomic Profiles in Lung Cancer Cell Invasion | Wang, Yi-Ting; Tsai, Chia-Feng; Hong, Tzu-Chan; Tsou, Chih-Chiang; Lin, Pei-Yi; Pan, Szu-Hua; Hong, Tse-Ming; Yang, Pan-Chyr; Sung, Ting-Yi ; Hsu, Wen-Lian ; Chen, Yu-Ju | JOURNAL OF PROTEOME RESEARCH 9(11), 5582-5597 | | | |
| 2012 | Complementary Fe3+- and Ti4+-immobilized metal ion affinity chromatography for purification of acidic and basic phosphopeptides | Lai, Alan Chuan-Ying; Tsai, Chia-Feng; Hsu, Chuan-Chih; Sun, Yu-Ni; Chen, Yu-Ju | RAPID COMMUNICATIONS IN MASS SPECTROMETRY 26, 2186-2194 | | | |
| 2010 | High-speed proteomic signature by informatics-assisted label-free quantitation | Lin, Pei-Yi; Tsai, Chia-Feng; Tsou, Chih-Chiang; Han, Chia-Li; Wang, Yi-Ting; Sung, Ting-Yi; Hsu, Wen-Lian; Chen, Yu-Ju | | | | |
| 2008 | High-speed Proteomic Signature by Swift LC-MS/MS and Label-free Quantitation | Lin, Pei-Yi; Tsai, Chia-feng; Tsou, Chih-Chiang; Wu, Chien-Peng; Wang, Yi-Ting; Sung, Ting-Yi; Hsu, Wen-Lian; Chen, Yu-Ju | | | | |
| 2008 | IDEAL-Q: An automated tool for high-performance label-free quantitative analysis | Tsou, Chih-Chiang; Tsai, Chia-Feng; Tsui, Ethan Yin-Hao; Yu, Paul Chuan-Yih; Wang, Yi-Ting; Lin, Pei-Yi; Chen, Yu-Ju; Sung, Ting-Yi; Hsu, Wen-Lian | | | | |
| 2010 | IDEAL-Q: An automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation | Tsou, Chih-Chiang; Tsai, Chia-Feng; Tsui, Ying-Hao; Sudhir, Putty-Reddy; Wang, Yi-Ting; Chen, Yu-Ju ; Chen, Jeou-Yuan ; Sung, Ting-Yi ; Hsu, Wen-Lian | Molecular and Cellular Proteomics 9(1), 131-144 | | | |
| 2008 | Immobilized Metal Affinity Chromatography Revisited: pH/acid Control toward High Selectivity in Phosphoproteomics | Tsai, Chia-Feng; Wang, Yi-Ting; Chen, Yet-Ran; Lai, Chen-Yu; Lin, Pei-Yi; Pan, Kuan-Ting; Chen, Jeou-Yuan ; Khoo, Kay-Hooi ; Chen, Yu-Ju | JOURNAL OF PROTEOME RESEARCH 7(9), 4058-4069 | | | |
| 2011 | Improving phosphorylation site assignment by statistical analysis | Lu, Sheng-Chieh; Tsai, Chia-Feng; Tsou, Chih-Chiang; Yang, Han-Yin; Chen, Lien-Chin; Chen, Yu-Ju; Sung, Ting-Yi; Hsu, Wen-Lian | | | | |
| 2010 | Improving phosphorylation site assignment by statistical analysis on CID fragmentation | Lu, Sheng-Shieh; Tsai, Chia-Feng; Tsou, Chih-Chiang; Yang, Han-Ying; Chen, Lien-Chin; Chen, Yu-Ju; Sung, Ting-Yi; Hsu, Wen-Lian | | | | |
| 2010 | Improving phosphorylation site assignment by statistical analysis on CID fragmentation | Lu, Sheng-Chieh; Tsai, Chia-Feng; Tsou, Chih-Chiang; Yang, Han-Yin; Chen, Lien-Chin; Chen, Yu-Ju; Sung, Ting-Yi; Hsu, Wen-Lian | | | | |
| 2018 | Inducing hair follicle neogenesis with secreted proteins enriched in embryonic skin | Fan, Sabrina Mai-Yi; Tsai, Chia-Feng; Yen, Chien-Mei; Lin, Miao-Hsia; Wang, Wei-Hung; Chan, Chih-Chieh; Chen, Chih-Lung; Phua, Kyle K.L.; Pan, Szu-Hua; Plikus, Maksim V.; Yu, Sung-Liang; Chen, Yu-Ju ; Lin, Sung-Jan | Biomaterials 167, 121-131 | | | |
| 2011 | Nanoprobe-based Immobilized Metal Affinity Chromatography for Sensitive and Complementary Enrichment of Multiply Phosphorylated Peptides | Wu, Huan-Ting; Hsu, Chuan-Chih; Tsai, Chia-Feng; Lin, Po-Chiao; Lin, Chun-Cheng; Chen, Yu-Ju | PROTEOMICS 13,11, 2639-2653 | | | |
| 2013 | ProtDIA-id: An automatic tool to extract MS/MS spectra for protein identification in proteomic experiments using data-independent acquisition | Chang, Hui-Yin; Chiang, Nai-Yuan; Tsai, Chia-Feng; Tsai, Ya-Wen; Chen, Yu-Ju; Sung, Ting-Yi; Hsu, Wen-Lian | | | | |
| 2008 | SEMI-quantitation Strategy for Label-free Quantitative Profiling of Phosphoproteome in Lung Cancer of Different Invasive Potential | Wang, Yi-Ting; Tsai, Chia-Feng; Lin, Pei-Yi; Hong, Tzu-Chan; Tsou, Chih-Chiang; Hsu, Wen-Lian; Sung, Ting-Yi; Hong, Tze Min; Yang, Pan-Chyr; Chen, Yu-Ju | | | | |
| 2013 | Spectrum-based method to generate good decoy libraries for spectral library searching in peptide identifications | Cheng, Chia-Ying; Tsai, Chia-Feng; Chen, Yu-Ju; Sung, Ting-Yi; Hsu, Wen-Lian | Journal of Proteome Research 12, 2305-2310 | | | |
