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1.Zhang, X.;? Cheng, K.;? Ning, Z.;? Mayne, J.;? Walker, K.;? Chi, H.;? Farnsworth, C. L.;? Lee, K.; Figeys, D., Exploring the Microbiome-Wide Lysine Acetylation, Succinylation, and Propionylation in Human Gut Microbiota. ANALYTICAL CHEMISTRY 2021, 93 (17), 6594-6598.?

2.Chen, Z.-L.;? Mao, P.-Z.;? Zeng, W.-F.;? Chi, H.; He, S.-M., pDeepXL: MS/MS Spectrum Prediction for Cross-Linked Peptide Pairs by Deep Learning. JOURNAL OF PROTEOME RESEARCH 2021, 20 (5), 2570-2582.?

3.Shao, G.-C;? Cao, Y;? Chen, Z.-L.;? Liu, C;? Li, S.-T.;? Chi, H.;? Dong, M.-Q., How to use open-pFind in deep proteomics data analysis?-A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data. Biophysics Reports 2021, 7 (3), 207-226.?

4.Wu, S.;? Sun, J.;? Wang, X.;? Xu, F.;? Chi, H.;? Li, Y.;? Zhong, B.;? Xie, Y.;? Yan, Z.;? Chang, L.;? Wang, D.;? He, F.;? Wu, J.;? Zhang, Y.; Xu, P., Open-pFind Verified Four Missing Proteins from Multi-Tissues. JOURNAL OF PROTEOME RESEARCH 2020, 19 (12), 4808-4814.?

5.Fei, Z.;? Wang, K.; Chi, H., GameTag: A New Sequence Tag Generation Algorithm Based on Cooperative Game Theory. PROTEOMICS 2020, 20 (21-22).?

6.Zhou, W.-J.;? Yang, H.;? Zeng, W.-F.;? Zhang, K.;? Chi, H.; He, S.-M., pValid: Validation Beyond the Target-Decoy Approach for Peptide Identification in Shotgun Proteomics. JOURNAL OF PROTEOME RESEARCH 2019, 18 (7), 2747-2758.?

7.Zhang, S.;? Cao, X.;? Liu, C.;? Li, W.;? Zeng, W.;? Li, B.;? Chi, H.;? Liu, M.;? Qin, X.;? Tang, L.;? Yan, G.;? Ge, Z.;? Liu, Y.;? Gao, Q.; Lu, H., N-glycopeptide Signatures of IgA2 in Serum from Patients with Hepatitis B Virus-related Liver Diseases. Molecular & cellular proteomics : MCP 2019, 18 (11), 2262-2272.?

8.Yang, H.;? Li, Y.-C.;? Zhao, M.-Z.;? Wu, F.-L.;? Wang, X.;? Xiao, W.-D.;? Wang, Y.-H.;? Zhang, J.-L.;? Wang, F.-Q.;? Xu, F.;? Zeng, W.-F.;? Overall, C. M.;? He, S.-M.;? Chi, H.; Xu, P., Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics. Molecular & cellular proteomics : MCP 2019, 18 (4), 773-785.?

9.Yang, H.;? Chi, H.;? Zeng, W.-F.;? Zhou, W.-J.; He, S.-M., pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework. BIOINFORMATICS 2019, 35 (14), I183-I190.?

10.Li, W.;? Chi, H.;? Salovska, B.;? Wu, C.;? Sun, L.;? Rosenberger, G.; Liu, Y., Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019, 30 (8), 1396-1405.?

11.Chen, Z.-L.;? Meng, J.-M.;? Cao, Y.;? Yin, J.-L.;? Fang, R.-Q.;? Fan, S.-B.;? Liu, C.;? Zeng, W.-F.;? Ding, Y.-H.;? Tan, D.;? Wu, L.;? Zhou, W.-J.;? Chi, H.;? Sun, R.-X.;? Dong, M.-Q.; He, S.-M., A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides. NATURE COMMUNICATIONS 2019, 10.?

12.Yang, H.;? Chi, H.;? Zhou, W.-J.;? Zeng, W.-F.;? Liu, C.;? Wang, R.-M.;? Wang, Z.-W.;? Niu, X.-N.;? Chen, Z.-L.; He, S.-M., pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization. JOURNAL OF PROTEOME RESEARCH 2018, 17 (1), 119-128.?

13.Chi, H.;? Liu, C.;? Yang, H.;? Zeng, W.-F.;? Wu, L.;? Zhou, W.-J.;? Wang, R.-M.;? Niu, X.-N.;? Ding, Y.-H.;? Zhang, Y.;? Wang, Z.-W.;? Chen, Z.-L.;? Sun, R.-X.;? Liu, T.;? Tan, G.-M.;? Dong, M.-Q.;? Xu, P.;? Zhang, P.-H.; He, S.-M., Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine. NATURE BIOTECHNOLOGY 2018, 36 (11), 1059-+.?

14.Zhou, X.-X.;? Zeng, W.-F.;? Chi, H.;? Luo, C.;? Liu, C.;? Zhan, J.; ?He, S.-M.; Zhang, Z., pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning. ANALYTICAL CHEMISTRY 2017, 89 (23), 12690-12697.?

15.Yang, H.;? Chi, H.;? Zhou, W.-J.;? Zeng, W.-F.;? He, K.;? Liu, C.;? Sun, R.-X.; He, S.-M., Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications. JOURNAL OF PROTEOME RESEARCH 2017, 16 (2), 645-654.?

16.Liu, M.-Q.;? Zeng, W.-F.;? Fang, P.;? Cao, W.-Q.;? Liu, C.;? Yan, G.-Q.;? Zhang, Y.;? Peng, C.;? Wu, J.-Q.;? Zhang, X.-J.;? Tu, H.-J.;? Chi, H.; ?Sun, R.-X.;? Cao, Y.;? Dong, M.-Q.;? Jiang, B.-Y.;? Huang, J.-M.;? Shen, H.-L.;? Wong, C. C. L.;? He, S.-M.; Yang, P.-Y., pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification. NATURE COMMUNICATIONS 2017, 8.?

17.Bu, S.-L.;? Liu, C.;? Liu, N.;? Zhao, J.-L.;? Ai, L.-F.;? Chi, H.;? Li, K. L.;? Chien, C.-W.;? Burlingame, A. L.;? Zhang, S.-W.; Wang, Z.-Y., Immunopurification and Mass Spectrometry Identifies Protein Phosphatase 2A (PP2A) and BIN2/GSK3 as Regulators of AKS Transcription Factors in Arabidopsis. MOLECULAR PLANT 2017, 10 (2), 345-348.?

18.Zeng, W.-F.;? Liu, M.-Q.;? Zhang, Y.;? Wu, J.-Q.;? Fang, P.;? Peng, C.;? Nie, A.;? Yan, G.;? Cao, W.;? Liu, C.;? Chi, H.;? Sun, R.-X.;? Wong, C. C. L.;? He, S.-M.; Yang, P., pGlyco: a pipeline for the identification of intact N-glycopeptides by using HCD-and CID-MS/MS and MS3. SCIENTIFIC REPORTS 2016, 6.?

19.Sun, R.-X.;? Luo, L.;? Wu, L.;? Wang, R.-M.;? Zeng, W.-F.;? Chi, H.;? Liu, C.; He, S.-M., pTop 1.0: A High-Accuracy and High-Efficiency Search Engine for Intact Protein Identification. ANALYTICAL CHEMISTRY 2016, 88 (6), 3082-3090.?

20.Zhang, K.;? Fu, Y.;? Zeng, W.-F.;? He, K.;? Chi, H.;? Liu, C.;? Li, Y.-C.;? Gao, Y.;? Xu, P.; He, S.-M., A note on the false discovery rate of novel peptides in proteogenomics. BIOINFORMATICS 2015, 31 (20), 3249-3253.?

21.Sun, R.-X.;? Luo, L.;? Chi, H.;? Liu, C.; He, S.-M., Top-down Proteomics: The Large-scale Proteoform Identification. PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS 2015, 42 (2), 101-114.?

22.Fan, S.-B.;? Meng, J.-M.;? Lu, S.;? Zhang, K.;? Yang, H.;? Chi, H.;? Sun, R.-X.;? Dong, M.-Q.; He, S.-M., Using pLink to Analyze Cross-Linked Peptides. Current protocols in bioinformatics 2015, 49, 8.21.1-8.21.19.?

23.Chi, H.;? He, K.;? Yang, B.;? Chen, Z.;? Sun, R.-X.;? Fan, S.-B.;? Zhang, K.;? Liu, C.;? Yuan, Z.-F.;? Wang, Q.-H.;? Liu, S.-Q.;? Dong, M.-Q.; He, S.-M., pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data (Reprinted from vol 125, pg 89-97, 2015). JOURNAL OF PROTEOMICS 2015, 129, 33-41.?

24.Su, Z.-D.;? Sheng, Q.-H.;? Li, Q.-R.;? Chi, H.;? Jiang, X.;? Yan, Z.;? Fu, N.;? He, S.-M.;? Khaitovich, P.;? Wu, J.-R.; Zeng, R., De novo identification and quantification of single amino-acid variants in human brain. JOURNAL OF MOLECULAR CELL BIOLOGY 2014, 6 (5), 421-433.?

25.Liu, C.;? Song, C.-Q.;? Yuan, Z.-F.;? Fu, Y.;? Chi, H.;? Wang, L.-H.;? Fan, S.-B.;? Zhang, K.;? Zeng, W.-F.;? He, S.-M.;? Dong, M.-Q.; Sun, R.-X., pQuant Improves Quantitation by Keeping out Interfering Signals and Evaluating the Accuracy of Calculated Ratios. ANALYTICAL CHEMISTRY 2014, 86 (11), 5286-5294.?

26.Fan, S.-B.;? Wu, Y.-J.;? Yang, B.;? Chi, H.;? Meng, J.-M.;? Lu, S.;? Zhang, K.;? Wu, L.;? Sun, R.-X.;? Dong, M.-Q.; He, S.-M., A New Approach to Protein Structure and Interaction Research: Chemical Cross-linking in Combination With Mass Spectrometry. PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS 2014, 41 (11), 1109-1125.?

27.Zhang, K.;? Wang, L.-H.;? Chi, H.;? Bu, D.-C.;? Yuan, Z.-F.;? Liu, C.;? Fan, S.-B.;? Chen, H.-F.;? Zeng, W.-F.;? Luo, H.-T.;? Sun, R.-X.;? He, S.-M.;? Xie, L.; Zhao, Y., Proteogenomics: Improving Genomes Annotation by Proteomics. PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS 2013, 40 (4), 297-308.?

28.Yuan, Z.-F.;? Wu, L.;? Liu, C.;? Chi, H.;? Fan, S.-B.;? Zhang, K.;? Zeng, W.-F.;? Sun, R.-X.; He, S.-M., Accurate Determination of Precursor Ions for Peptides in Large-scale Protein Identification. PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS 2013, 40 (1), 80-92.?

29.Chi, H.;? Chen, H.;? He, K.;? Wu, L.;? Yang, B.;? Sun, R.-X.;? Liu, J.;? Zeng, W.-F.;? Song, C.-Q.;? He, S.-M.; Dong, M.-Q., pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra. JOURNAL OF PROTEOME RESEARCH 2013, 12 (2), 615-625.?

30.Yuan, Z.-F.;? Liu, C.;? Wang, H.-P.;? Sun, R.-X.;? Fu, Y.;? Zhang, J.-F.;? Wang, L.-H.;? Chi, H.;? Li, Y.;? Xiu, L.-Y.;? Wang, W.-P.; He, S.-M., pParse: A method for accurate determination of monoisotopic peaks in high-resolution mass spectra. PROTEOMICS 2012, 12 (2), 226-235.?

31.Ye, D.;? Fu, Y.;? Sun, R.-X.;? Wang, H.-P.;? Yuan, Z.-F.;? Chi, H.; He, S.-M., Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate. BIOINFORMATICS 2010, 26 (12), i399-i406.?

32.Sun, R.-X.;? Dong, M.-Q.;? Song, C.-Q.;? Chi, H.;? Yang, B.;? Xiu, L.-Y.;? Tao, L.;? Jing, Z.-Y.;? Liu, C.;? Wang, L.-H.;? Fu, Y.; He, S.-M., Improved Peptide Identification for Proteomic Analysis Based on Comprehensive Characterization of Electron Transfer Dissociation Spectra. JOURNAL OF PROTEOME RESEARCH 2010, 9 (12), 6354-6367.?

33.Liu, C.;? Wang, H.;? Fu, Y.;? Yuan, Z.;? Chi, H.;? Wang, L.;? Sun, R.; He, S., [Prediction of peptide retention time in reversed-phase liquid chromatography and its application in protein identification]. Se pu = Chinese journal of chromatography 2010, 28 (6), 529-34.?

34.Li, Y.;? Chi, H.;? Wang, L.-H.;? Wang, H.-P.;? Fu, Y.;? Yuan, Z.-F.;? Li, S.-J.;? Liu, Y.-S.;? Sun, R.-X.;? Zeng, R.; He, S.-M., Speeding up tandem mass spectrometry based database searching by peptide and spectrum indexing. RAPID COMMUNICATIONS IN MASS SPECTROMETRY 2010, 24 (6), 807-814.?

35.Chi, H.;? Sun, R.-X.;? Yang, B.;? Song, C.-Q.;? Wang, L.-H.;? Liu, C.;? Fu, Y.;? Yuan, Z.-F.;? Wang, H.-P.;? He, S.-M.; Dong, M.-Q., pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra. JOURNAL OF PROTEOME RESEARCH 2010, 9 (5), 2713-2724.?

36.Fu, Y.;? Jia, W.;? Lu, Z.;? Wang, H.;? Yuan, Z.;? Chi, H.;? Li, Y.;? Xiu, L.;? Wang, W.;? Liu, C.;? Wang, L.;? Sun, R.;? Gao, W.;? Qian, X.; He, S.-M., Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences. BMC BIOINFORMATICS 2009, 10.?