Citation: XIAO Kaijie, TIAN Zhixin. Top-down characterization of histone H4 proteoforms with ProteinGoggle 2.0[J]. Chinese Journal of Chromatography, ;2016, 34(12): 1255-1263. doi: 10.3724/SP.J.1123.2016.09012 shu

Top-down characterization of histone H4 proteoforms with ProteinGoggle 2.0

XIAO Kaijie ,
TIAN Zhixin

School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China

Received Date: 4 September 2016

Fund Project: China State Key Basic Research Program (No. 2013CB911203)National Natural Science Foundation of China (No. 21575104) Shanghai Science and Technology Commission (No. 14DZ2261100).

Top-down characterization of combinatorial and dense post-translational modifications (PTMs) on core histones has long been a big analytical challenge because of enormous putative proteoforms for identification and simultaneously enormous putative sites of each individual PTM for localization. ProteinGoggle 2.0, as implemented with the isotopic mass-to-charge ratio and envelope fingerprinting algorithm, has multiple unique strengths for top-down characterization of histone PTMs together with high-resolution tandem mass spectrometry. Here we report our database search and proteoform identification of HeLa core histone H4 using ProteinGoggle 2.0. The Theoretical database containing all putative proteoforms was created with shotgun annotation from the human H4 flat text downloaded from UniProt; information including the amino acid sequence, putative PTMs (methylation, di-methylation, tri-methylation, acetylation and phosphorylation) and amino acid variation (A77 to P) was adopted from the flat text file. A total of 426 proteoforms were confidently identified with a spectrum level false discovery rate of less than 1%, which represents the most comprehensive H4 proteoforms reported so far. Side-by-side comparison of these proteoforms with those identified by ProSightPC 2.0 was also made. By and large, ProteinGoggle 2.0 can be adopted for database search and proteoform identification of proteins with multiple combinatorial PTMs as well as amino acid variation.
- ProteinGoggle 2.0,
- top-down,
- histone H4,
- proteoform
1. [1]
2. [2]
3. [3]
4. [4]
5. [5]
6. [6]
7. [7]
8. [8]
9. [9]
10. [10]
11. [11]
12. [12]
13. [13]
14. [14]
15. [15]
16. [16]
17. [17]
18. [18]
19. [19]
20. [20]
21. [21]
22. [22]
23. [23]
1. [1]
  Zhi Zheng , Feiyang Liu , Junlong Zhao . D-Amino Acids and Mirror-Image Proteins. University Chemistry, 2026, 41(2): 353-359. doi: 10.12461/PKU.DXHX202505017
2. [2]
  Xinran Zhang , Siqi Liu , Yichi Chen , Qingli Zou , Qinghong Xu , Yaqin Huang . From Protein to Energy Storage Materials: Edible Gelatin Jelly Electrolyte. University Chemistry, 2025, 40(7): 255-266. doi: 10.12461/PKU.DXHX202408104
3. [3]
  Xinyi Hong , Tailing Xue , Zhou Xu , Enrong Xie , Mingkai Wu , Qingqing Wang , Lina Wu . Non-Site-Specific Fluorescent Labeling of Proteins as a Chemical Biology Experiment. University Chemistry, 2024, 39(4): 351-360. doi: 10.3866/PKU.DXHX202310010
4. [4]
  Yongjie ZHANG , Bintong HUANG , Yueming ZHAI . Research progress of formation mechanism and characterization techniques of protein corona on the surface of nanoparticles. Chinese Journal of Inorganic Chemistry, 2024, 40(12): 2318-2334. doi: 10.11862/CJIC.20240247
5. [5]
  Zeyu XU , Anlei DANG , Bihua DENG , Xiaoxin ZUO , Yu LU , Ping YANG , Wenzhu YIN . Evaluation of the efficacy of graphene oxide quantum dots as an ovalbumin delivery platform and adjuvant for immune enhancement. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1065-1078. doi: 10.11862/CJIC.20240099
6. [6]
  Yanfen PENG , Xinyue WANG , Tianbao LIU , Xiaoshuo WU , Yujing WEI . Syntheses and luminescence of four Cd(Ⅱ)/Zn(Ⅱ) complexes constructed by 1,3‐bis(4H‐1,2,4‐triazole)benzene. Chinese Journal of Inorganic Chemistry, 2025, 41(7): 1416-1426. doi: 10.11862/CJIC.20250018
7. [7]
  Miao-Bin Xu , Qian-Qian Chen , Bing-Xuan Li , Ke-Zhao Du , Jin Chen . π-Lone pair synergy in (C₇H₄NO₄)(IO₃): Optimal balance among SHG, birefringence, and bandgap performance. Chinese Chemical Letters, 2025, 36(11): 110513-. doi: 10.1016/j.cclet.2024.110513
8. [8]
  Gang Hu , Chun Wang , Qinqin Wang , Mingyuan Zhu , Lihua Kang . The controlled oxidation states of the H₄PMo₁₁VO₄₀ catalyst induced by plasma for the selective oxidation of methacrolein. Chinese Chemical Letters, 2025, 36(2): 110298-. doi: 10.1016/j.cclet.2024.110298
9. [9]
  Xiaodong Zhang , Bohui Xu , Deshuai Xiao , Xinyuan Zhang , Pifu Gong , Zheshuai Lin . From centrosymmetric CN3H6C6H5SO3 to non-centrosymmetric CN3H6C6H4SO3(OH): Hydroxyl introduced hydrogen bond reconstruction to realize strong second harmonic generation. Chinese Journal of Structural Chemistry, 2025, 44(10): 100707-100707. doi: 10.1016/j.cjsc.2025.100707
10. [10]
  Ke-Ai Zhou , Lian Huang , Xing-Ping Fu , Li-Ling Zhang , Yu-Ling Wang , Qing-Yan Liu . Fluorinated metal-organic framework for methane purification from a ternary CH4/C2H6/C3H8 mixture. Chinese Journal of Structural Chemistry, 2023, 42(11): 100172-100172. doi: 10.1016/j.cjsc.2023.100172
11. [11]
  Lihui Ou , Zhancheng Liu , Dai-Huo Liu , Zhi Zhang . Cl-adsorbed Cu(111)/H₂O interface selectively realizes electrochemical CO₂ reduction towards C₂H₄ product: Mechanistic understanding. Chinese Chemical Letters, 2026, 37(2): 111920-. doi: 10.1016/j.cclet.2025.111920
12. [12]
  Chengxin Chen , Hongfei Shi , Xiaoyan Cai , Liang Mao , Zhe Chen . Enhanced bifunctional photocatalytic performances for H₂ evolution and HCHO elimination with an S-scheme CoWO₄/CdIn₂S₄ heterojunction. Acta Physico-Chimica Sinica, 2025, 41(12): 100155-0. doi: 10.1016/j.actphy.2025.100155
13. [13]
  Gaofeng WANG , Shuwen SUN , Yanfei ZHAO , Lixin MENG , Bohui WEI . Structural diversity and luminescence properties of three zinc coordination polymers based on bis(4-(1H-imidazol-1-yl)phenyl)methanone. Chinese Journal of Inorganic Chemistry, 2024, 40(5): 849-856. doi: 10.11862/CJIC.20230479
14. [14]
  Sikai Wu , Xuefei Wang , Huogen Yu . Hydroxyl-enriched hydrous tin dioxide-coated BiVO4 with boosted photocatalytic H2O2 production. Chinese Journal of Structural Chemistry, 2024, 43(12): 100457-100457. doi: 10.1016/j.cjsc.2024.100457
15. [15]
  Hualin Jiang , Wenxi Ye , Huitao Zhen , Xubiao Luo , Vyacheslav Fominski , Long Ye , Pinghua Chen . Novel 3D-on-2D g-C₃N₄/AgI._x._y heterojunction photocatalyst for simultaneous and stoichiometric production of H₂ and H₂O₂ from water splitting under visible light. Chinese Chemical Letters, 2025, 36(2): 109984-. doi: 10.1016/j.cclet.2024.109984
16. [16]
  Dong-Xue Jiao , Hui-Li Zhang , Chao He , Si-Yu Chen , Ke Wang , Xiao-Han Zhang , Li Wei , Qi Wei . Layered (C5H6ON)2[Sb2O(C2O4)3] with a large birefringence derived from the uniform arrangement of π-conjugated units. Chinese Journal of Structural Chemistry, 2024, 43(6): 100304-100304. doi: 10.1016/j.cjsc.2024.100304
17. [17]
  Tong Zhou , Xue Liu , Liang Zhao , Mingtao Qiao , Wanying Lei . Efficient Photocatalytic H₂O₂ Production and Cr(Ⅵ) Reduction over a Hierarchical Ti₃C₂/In₄SnS₈ Schottky Junction. Acta Physico-Chimica Sinica, 2024, 40(10): 2309020-0. doi: 10.3866/PKU.WHXB202309020
18. [18]
  Guoqiang Chen , Zixuan Zheng , Wei Zhong , Guohong Wang , Xinhe Wu . Molten Intermediate Transportation-Oriented Synthesis of Amino-Rich g-C₃N₄ Nanosheets for Efficient Photocatalytic H₂O₂ Production. Acta Physico-Chimica Sinica, 2024, 40(11): 2406021-0. doi: 10.3866/PKU.WHXB202406021
19. [19]
  Wei Zhong , Dan Zheng , Yuanxin Ou , Aiyun Meng , Yaorong Su . Simultaneously Improving Inter-Plane Crystallization and Incorporating K Atoms in g-C₃N₄ Photocatalyst for Highly-Efficient H₂O₂ Photosynthesis. Acta Physico-Chimica Sinica, 2024, 40(11): 2406005-0. doi: 10.3866/PKU.WHXB202406005
20. [20]
  Zheng Liu , Yuqing Bian , Graham Dawson , Jiawei Zhu , Kai Dai . Rational constructing of Zn_0.5Cd_0.5S-diethylenetriamine/g-C₃N₄ S-scheme heterojunction with enhanced photocatalytic H₂O₂ production. Chinese Chemical Letters, 2025, 36(9): 111272-. doi: 10.1016/j.cclet.2025.111272

Get Citation

PDF

XML

Metrics

PDF Downloads(6)
Abstract views(815)
HTML views(146)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142