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Comparative Analysis of Chemical Cross-Linking Mass Spectrometry Data Indicates That Protein STY Residues Rarely React with N-Hydroxysuccinimide Ester Cross-Linkers 期刊论文
JOURNAL OF PROTEOME RESEARCH, 2023, 卷号: 22, 期号: 8, 页码: 2593-2607
作者:  Cao, Yong;  Liu, Xin-Tong;  Mao, Peng-Zhi;  Chen, Zhen-Lin;  Tarn, Ching;  Dong, Meng-Qiu
收藏  |  浏览/下载:7/0  |  提交时间:2023/12/04
CXMS  XL-MS  NHS ester cross-linker  pLink  xiSearch  MeroX  
pDeepXL: MS/MS Spectrum Prediction for Cross-Linked Peptide Pairs by Deep Learning 期刊论文
JOURNAL OF PROTEOME RESEARCH, 2021, 卷号: 20, 期号: 5, 页码: 2570-2582
作者:  Chen, Zhen-Lin;  Mao, Peng-Zhi;  Zeng, Wen-Feng;  Chi, Hao;  He, Si-Min
收藏  |  浏览/下载:39/0  |  提交时间:2021/12/01
cross-linking mass spectrometry  spectrum prediction  deep learning  transfer learning  online fine-tuning  
Open-pFind Verified Four Missing Proteins from Multi-Tissues 期刊论文
JOURNAL OF PROTEOME RESEARCH, 2020, 卷号: 19, 期号: 12, 页码: 4808-4814
作者:  Wu, Shujia;  Sun, Jinshuai;  Wang, Xi;  Xu, Feng;  Chi, Hao;  Li, Yanchang;  Zhong, Bowen;  Xie, Yuping;  Yan, Zhonghua;  Chang, Lei;  Wang, Dongxue;  He, Fuchu;  Wu, Junzhu;  Zhang, Yao;  Xu, Ping
收藏  |  浏览/下载:39/0  |  提交时间:2021/12/01
Chromosome-Centric Human Proteome Project  missing proteins  open-pFind  multiple tissues  
pValid: Validation Beyond the Target-Decoy Approach for Peptide Identification in Shotgun Proteomics 期刊论文
JOURNAL OF PROTEOME RESEARCH, 2019, 卷号: 18, 期号: 7, 页码: 2747-2758
作者:  Zhou, Wen-Jing;  Yang, Hao;  Zeng, Wen-Feng;  Zhang, Kun;  Chi, Hao;  He, Si-Min
收藏  |  浏览/下载:247/0  |  提交时间:2019/08/16
tandem mass spectrometry  target-decoy approach  validation methods  false-positive rate  false-negative rate  
Global Quantification of Intact Proteins via Chemical Isotope Labeling and Mass Spectrometry 期刊论文
JOURNAL OF PROTEOME RESEARCH, 2019, 卷号: 18, 期号: 5, 页码: 2185-2194
作者:  Liu, Zheyi;  Wang, Ruimin;  Liu, Jing;  Sun, Ruixiang;  Wang, Fangjun
收藏  |  浏览/下载:73/0  |  提交时间:2019/08/16
mass spectrometry  chemical isotope labeling  intact protein quantification  pTOP  highest isotopic peak  
pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization 期刊论文
JOURNAL OF PROTEOME RESEARCH, 2018, 卷号: 17, 期号: 1, 页码: 119-128
作者:  Yang, Hao;  Chi, Hao;  Zhou, Wen-Jing;  Zeng, Wen-Feng;  Liu, Chao;  Wang, Rui-Min;  Wang, Zhao-Wei;  Niu, Xiu-Nan;  Chen, Zhen-Lin;  He, Si-Min
收藏  |  浏览/下载:71/0  |  提交时间:2019/12/10
tandem mass spectrometry  de novo peptide sequencing  modification site localization  phosphorylation  
Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications 期刊论文
JOURNAL OF PROTEOME RESEARCH, 2017, 卷号: 16, 期号: 2, 页码: 645-654
作者:  Yang, Hao;  Chi, Hao;  Zhou, Wen-Jing;  Zeng, Wen-Feng;  He, Kun;  Liu, Chao;  Sun, Rui-Xiang;  He, Si-Min
收藏  |  浏览/下载:50/0  |  提交时间:2019/12/12
tandem mass spectrometry  de novo peptide sequencing  dynamic programming  unexpected modifications  
Pulsed Azidohomoalanine Labeling in Mammals (PALM) Detects Changes in Liver-Specific LKB1 Knockout Mice 期刊论文
JOURNAL OF PROTEOME RESEARCH, 2015, 卷号: 14, 期号: 11, 页码: 4815-4822
作者:  McClatchy, Daniel B.;  Ma, Yuanhui;  Liu, Chao;  Stein, Benjamin D.;  Martinez-Bartolome, Salvador;  Vasquez, Debbie;  Hellberg, Kristina;  Shaw, Reuben J.;  Yates, John R., III
收藏  |  浏览/下载:42/0  |  提交时间:2019/12/13
azidohomoalanine  newly synthesized proteins  proteomics  mass spectrometry  BONCAT  LKB1  quantitation  
pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra 期刊论文
JOURNAL OF PROTEOME RESEARCH, 2010, 卷号: 9, 期号: 5, 页码: 2713-2724
作者:  Chi, Hao;  Sun, Rui-Xiang;  Yang, Bing;  Song, Chun-Qing;  Wang, Le-Heng;  Liu, Chao;  Fu, Yan;  Yuan, Zuo-Fei;  Wang, Hai-Peng;  He, Si-Min;  Dong, Meng-Qiu
收藏  |  浏览/下载:60/0  |  提交时间:2019/12/16
tandem mass spectrometry  HCD  de novo sequencing  pNovo  
Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra 期刊论文
JOURNAL OF PROTEOME RESEARCH, 2008, 卷号: 7, 期号: 1, 页码: 202-208
作者:  Sun, Shiwei;  Yu, Chungong;  Qiao, Yantao;  Lin, Yu;  Dong, Gongjin;  Liu, Changning;  Zhang, Lingfen;  Zhang, Zhuo;  Cai, Jinjin;  Zhang, Hong;  Bu, Dongbo
收藏  |  浏览/下载:38/0  |  提交时间:2019/12/16
protein identification  tandem mass spectrum  expectation-maximization  neutral loss probability