期刊文章: 

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.