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(1) Lou, R.; Tang, P.; Ding, K.; Li, S.; Tian, C.; Li,Y.; Zhao, S.; Zhang, Y.*; Shui, W.* Hybrid Spectral Library Combining DIA-MS Data and a Targeted Virtual Library Substantially Deepens the Proteome Coverage. iScience 2020, 23(3): 100903.

(2) Sun, Y.; Hou, S.; Zhao, K.; Long, H.; Liu, Z.; Gao,J.; Zhang, Y.; Su, X.; Li, D.*; Liu, C.* Cryo-EM structure of full-length α-synuclein amyloid fibril with Parkinson’s disease familial A53T mutation. Cell Res 2020.

(3) Guo, L.; Gao, J.; Gao, Y.; Zhu, Z.; Zhang, Y.* Aspirin reshapes acetylomesin inflammatory and cancer cells via CoA-dependent and -independent pathways. J Proteome Res 2020.

(4) Yang, L.; Cao, Y.; Zhao, J.; Fang, Y.; Liu, N.*; Zhang, Y.* Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signalsfor Normal Aging and Age-associated Disease in Drosophila. Mol Cell Proteomics 2019, 18(10): 2078-2088.

(5) Yang, L.; Ma, Z.; Wang, H.; Niu, K.; Cao, Y.; Sun, L.; Geng, Y.; Yang, B.; Gao, F.; Chen, Z.; Wu, Z.;  Li, Q.; Shen, Y.; Zhang, X.; Jiang, H.; Chen, Y.; Liu, R.; Liu, N.*; Zhang, Y.* Ubiquitylome study identifies increased histone 2A ubiquitylation as an evolutionarily conserved aging biomarker. Nat Commun 2019, 10, 2191.

(6) Qiang, J.; Ma, Z.; Xie, X.; Shi, L.; Geng, Y.; Hu, J.; Liu, R.; Liu, N.; Zhang, Y.* Multi-omic Analyses Reveal Minimal Impact of the CRISPR-Cas9 Nuclease on Cultured Human Cells. J Proteome Res 2019, 18, 1054-1063.

(7) Ma, Z.; Wang, H.; Cai, Y.; Wang, H.; Niu, K.; Wu, X.; Ma, H.; Yang, Y.; Tong, W.; Liu, F.; Liu, Z.; Zhang, Y.; Liu, R.; Zhu, Z. J.*; Liu, N.* Epigenetic drift of H3K27me3 in aging links glycolysis to healthy longevity in Drosophila. Elife 2018, 7.

(8) Guo, L.; Yang, W.; Huang, Q.; Qiang, J.; Hart, J. R.; Wang, W.; Hu, J.; Zhu, Z. J.; Liu, N.; Zhang, Y.* Selenocysteine-Specific Mass Spectrometry Reveals Tissue-Distinct Selenoproteomes and Candidate Selenoproteins. Cell Chem Biol 2018, 25, 1380-1388.

(9) Yang, X.; Wang, Z.; Guo, L.; Zhu, Z. J.; Zhang,Y.* Proteome-Wide Analysis of N-Glycosylation Stoichiometry Using SWATH Technology. J Proteome Res 2017, 16, 3830-3840.

(10) Mu, R.; Tat, J.; Zamudio, R.; Zhang, Y.; Yates, J. R., 3rd; Kumagai, A.; Dunphy, W. G.; Reed, S. I.* CKS Proteins Promote Checkpoint Recovery by Stimulating Phosphorylation of Treslin. Mol CellBiol 2017, 37.

(11) Jin, H. Y.; Oda, H.; Chen, P.; Yang, C.; Zhou, X.; Kang, S. G.; Valentine, E.; Kefauver, J. M.; Liao, L.; Zhang, Y.; Gonzalez-Martin, A.; Shepherd, J.; Morgan, G. J.; Mondala, T. S.; Head, S.R.; Kim, P. H.; Xiao, N.; Fu, G.; Liu, W. H.; Han, J.; Williamson, J. R.; Xiao,C.* Differential Sensitivity of Target Genes to Translational Repression by miR-17~92. PLoS Genet 2017, 13, e1006623.

(12) Wang, H.; Ma, Z.; Niu, K.; Xiao, Y.; Wu, X.; Pan, C.; Zhao, Y.; Wang, K.; Zhang, Y.; Liu, N.* Antagonistic roles of Nibbler and Hen1 in modulating piRNA 3' ends in Drosophila. Development 2016,143, 530-539.

(13) Pedros, C.; Zhang, Y.; Hu, J. K.; Choi, Y.S.; Canonigo-Balancio, A. J.; Yates, J. R., 3rd; Altman, A.; Crotty, S.; Kong, K. F.* A TRAF-like motif of the inducible costimulator ICOS controls development of germinal center TFH cells via the kinase TBK1. NatImmunol 2016, 17, 825-833.

(14) Zhang, Y.; Xu, T.; Shan, B.; Hart, J.; Aslanian, A.; Han, X.; Zong, N.; Li, H.; Choi, H.; Wang, D.; Acharya, L.; Du, L.; Vogt, P. K.; Ping, P.; Yates, J. R., 3rd.* Protein Inferencer: Confident protein identification and multiple experiment comparison for large scale proteomics projects. J Proteomics 2015, 129, 25-32.

(15) Xia, H. G.; Najafov, A.; Geng, J.; Galan-Acosta, L.; Han, X.; Guo, Y.; Shan, B.; Zhang, Y.; Norberg, E.; Zhang, T.; Pan, L.; Liu, J.; Coloff, J. L.; Ofengeim, D.; Zhu, H.; Wu, K.; Cai, Y.; Yates, J.R., 3rd; Zhu, Z. J.; Yuan, J.*; Vakifahmetoglu-Norberg, H. Degradation of HK2 by chaperone-mediated autophagy promotes metabolic catastrophe and cell death. J Cell Biol 2015, 210, 705-716.

(16) Tang, B.; Wang, T.; Wan, H.; Han, L.; Qin, X.; Zhang, Y.; Wang, J.; Yu, C.; Berton, F.; Francesconi, W.; Yates, J. R., 3rd; Vanderklish, P. W.; Liao, L.* Fmr1 deficiency promotes age-dependent alterations in the cortical synaptic proteome. Proc Natl Acad Sci U S A 2015,112, E4697-4706.

(17) Ofengeim, D.; Ito, Y.; Najafov, A.; Zhang, Y.; Shan, B.; DeWitt, J. P.; Ye, J.; Zhang, X.; Chang, A.; Vakifahmetoglu-Norberg, H.; Geng, J.; Py, B.; Zhou, W.; Amin, P.; Berlink Lima, J.; Qi, C.; Yu, Q.; Trapp, B.; Yuan, J.* Activation of necroptosis in multiple sclerosis. Cell Rep 2015, 10, 1836-1849.

(18) Huang, Q.; Yang, L.; Luo, J.; Guo, L.; Wang, Z.; Yang, X.; Jin, W.; Fang, Y.; Ye, J.; Shan, B.; Zhang, Y.* SWATH enables precise label-free quantification on proteome scale. Proteomics 2015, 15, 1215-1223.

(19) Hassler, J. R.; Scheuner, D. L.; Wang, S.; Han, J.; Kodali, V. K.; Li, P.; Nguyen, J.; George, J. S.; Davis, C.; Wu, S. P.; Bai,Y.; Sartor, M.; Cavalcoli, J.; Malhi, H.; Baudouin, G.; Zhang, Y.; Yates, J. R., 3rd; Itkin-Ansari, P.; Volkmann, N.; Kaufman, R. J.* The IRE1alpha/XBP1s Pathway Is Essential for the Glucose Response and Protection of beta Cells. PLoS Biol 2015, 13, e1002277.

(20) Hart, J. R.; Zhang, Y.; Liao, L.; Ueno, L.; Du, L.; Jonkers, M.; Yates, J. R., 3rd; Vogt, P. K.* The butterfly effect in cancer: a single base mutation can remodel the cell. Proc Natl Acad Sci U S A 2015, 112, 1131-1136.

(21) Zhang, Y.; Shan, B.; Boyle, M.; Liu, J.; Liao, L.; Xu, T.; Yates, J. R., 3rd.* Brain Proteome Changes Induced by Olfactory Learning in Drosophila. J Proteome Res 2014, 13, 3763-3770.

(22) Shan, B.; Xu, C.; Zhang, Y.; Xu, T.; Gottesfeld, J. M.; Yates, J. R., 3rd.* Quantitative proteomic analysis identifies targets and pathways of a 2-aminobenzamide HDAC inhibitor in Friedreich's ataxia patient iPSC-derived neural stem cells. J Proteome Res 2014, 13, 4558-4566.

(23) Kong, K. F.; Fu, G.; Zhang, Y.; Yokosuka, T.; Casas, J.; Canonigo-Balancio, A. J.; Becart, S.; Kim, G.; Yates, J. R., 3rd; Kronenberg, M.; Saito, T.; Gascoigne, N. R.; Altman, A.* Protein kinase C-eta controls CTLA-4-mediated regulatory T cell function. Nat Immunol 2014, 15, 465-472.

(24) Zhang, Y.; Fonslow, B. R.; Shan, B.; Baek, M. C.; Yates, J. R., 3rd.* Protein analysis by shotgun/bottom-upproteomics. Chem Rev 2013, 113, 2343-2394.

(25) Webhofer, C.; Zhang, Y.; Brusis, J.; Reckow, S.; Landgraf, R.; Maccarrone, G.; Turck, C. W.; Filiou, M. D.* (1)(5)Nmetabolic labeling: evidence for a stable isotope effect on plasma protein levels and peptide chromato graphic retention times. J Proteomics 2013, 88, 27-33.

(26) Ryan, S. D.; Dolatabadi, N.; Chan, S. F.; Zhang, X.; Akhtar, M. W.; Parker, J.; Soldner, F.; Sunico, C. R.; Nagar, S.; Talantova, M.; Lee, B.; Lopez, K.; Nutter, A.; Shan, B.; Molokanova, E.; Zhang, Y.; Han, X.; Nakamura, T.; Masliah, E.; Yates, J. R., 3rd; Nakanishi, N.; Andreyev, A. Y.; Okamoto, S.; Jaenisch, R.*; Ambasudhan, R.*; Lipton, S. A.* Isogenic human iPSC Parkinson's model shows nitrosative stress-induced dysfunction inMEF2-PGC1 alpha transcription. Cell 2013, 155, 1351-1364.

(27) Filiou, M. D.; Webhofer, C.; Gormanns, P.; Zhang, Y.; Reckow, S.; Bisle, B.; Teplytska, L.; Frank, E.; Kessler, M. S.; Maccarrone, G.; Landgraf, R.; Turck, C. W.* The (15)N isotope effect as a means for correlating phenotypic alterations and affected pathways in a trait anxiety mouse model. Proteomics 2012, 12, 2421-2427.

(28) Zhang, Y.; Reckow, S.; Webhofer, C.; Boehme, M.; Gormanns, P.; Egge-Jacobsen, W. M.; Turck, C. W.* Proteome scale turnover analysis in live animals using stable isotope metabolic labeling. AnalChem 2011, 83, 1665-1672.

(29) Zhang, Y.; Filiou, M. D.; Reckow, S.; Gormanns, P.; Maccarrone, G.; Kessler, M. S.; Frank, E.; Hambsch, B.; Holsboer, F.; Landgraf, R.; Turck, C. W.* Proteomic and metabolomic profiling of a trait anxiety mouse model implicate affected pathways. Mol Cell Proteomics 2011, 10, M111008110.

(30) Filiou, M. D.; Zhang, Y.; Teplytska, L.; Reckow, S.; Gormanns, P.; Maccarrone, G.; Frank, E.; Kessler, M. S.; Hambsch, B.; Nussbaumer, M.; Bunck, M.; Ludwig, T.; Yassouridis, A.; Holsboer, F.; Landgraf, R.; Turck, C. W.* Proteomics and metabolomics analysis of a trait anxiety mouse model reveals divergent mitochondrial pathways. BiolPsychiatry 2011, 70, 1074-1082.

(31) Zhang, Y.; Webhofer, C.; Reckow, S.; Filiou, M. D.; Maccarrone, G.; Turck, C. W.* A MS data search method for improved 15N-labeled protein identification. Proteomics 2009, 9, 4265-4270.

(32) Haegler, K.; Mueller, N. S.; Maccarrone, G.; Hunyadi-Gulyas, E.; Webhofer, C.; Filiou, M. D.; Zhang, Y.; Turck, C. W.* Quanti Spec--Quantitative mass spectrometry data analysis of (15)N-metabolically labeled proteins. J Proteomics 2009, 71, 601-608.

(33) Frank, E.; Kessler, M. S.; Filiou, M. D.; Zhang,Y.; Maccarrone, G.; Reckow, S.; Bunck, M.; Heumann, H.; Turck, C. W.; Landgraf, R.; Hambsch, B.* Stable isotope metabolic labeling with a novel N-enriched bacteria diet for improved proteomic analyses of mouse models for psychopathologies. PLoS One 2009, 4, e7821.


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