Citation: LU Wenyuan, ZHANG Yang, SHEN Chengpin, YIN Xuefei, LIU Xiaohui, YANG Pengyuan. A method using spectrum alignment to improve analysis efficiency of liquid chromatography combined with mass spectrometry[J]. Chinese Journal of Chromatography, ;2014, 32(4): 349-354. doi: 10.3724/SP.J.1123.2013.10030 shu

A method using spectrum alignment to improve analysis efficiency of liquid chromatography combined with mass spectrometry

1.
1. Department of Chemistry, Fudan University, Shanghai 200433, China;

Corresponding author: YANG Pengyuan,
Received Date: 29 October 2013
Available Online: 28 November 2013
Fund Project: 国家重大科学计划项目(2010CB912700，2013CB911201，2011CB910600)；国家高技术研究发展计划项目(2012AA020203，2014AAQ00361)；国家自然科学基金重点项目(21227805). (2010CB912700，2013CB911201，2011CB910600)；国家高技术研究发展计划项目(2012AA020203，2014AAQ00361)；国家自然科学基金重点项目(21227805)

In the analysis of proteins in human umbilical vein endothelial cells (HUVEC) treated with dimethyl sulfoxide (DMSO) and NEDD8-activating enzyme inhibitor (MLN4924,MLN), the Progenesis LC-MS software (Nonlinear Dynamics Ltd) was applied to liquid chromatography spectrum alignment, while spectrum similarities were figured out among several experiments of the same sample, and also among different samples. After double enzymolysis, the sample was added with digested QconCAT standard proteins. They were separated by HPLC-MS/MS, followed by spectrum alignment and data analysis. This established experiment flow offered a better identification result of more than 8000 proteins, while the original result was about 7000 proteins, ensuring a relatively high identification efficiency. On the basis of relative quantification with spectrum count, the described procedure can analyze the differential expression of proteins induced by DMSO and MLN. The similarities of total ion chromatograms after alignment were also compared. This method was proved to be quick and easy, with the advantages of high throughput and high sensitivity.
- high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS),
- spectrum alignment,
- protein analysis
1. [1]
  [1] Wang P, Tang H, Fitzgibbon M P, et al. Biostatistics, 2007, 8(2): 357
2. [2]
  [2] Kim S, Mischerikow N, Bandeira N, et al. Mol Cell Proteomics, 2010, 9(12): 2840
3. [3]
  [3] Nielsen N P V, Carstensen J M, Smedsgaard J. J Chromatogr A, 1998, 805(1): 17
4. [4]
  [4] Wang S, Yao J, Liu J, et al. Medical Physics, 2009, 36(12): 5595
5. [5]
  [5] May D, Law W, Fitzgibbon M, et al. J Proteome Res, 2009, 8(6): 3212
6. [6]
  [6] Li X J, Yi E C, Kemp C J, et al. Mol Cell Proteomics, 2005, 4(9): 1328
7. [7]
  [7] Fugmann T, Neri D, Roesli C. Proteomics, 2010, 10(14): 2631
8. [8]
  [8] Katajamaa M, Oresic M. BMC Bioinformatics, 2005, 6(1): 179
9. [9]
  [9] Fraga C G, Prazen B J, Synovec R E. Anal Chem, 2001, 73(24): 5833
10. [10]
  [10] Yu Y J, Wu H L, Fu H Y, et al. J Chromatogr A, 2013, 1302: 72
11. [11]
  [11] Ramaker H J, van Sprang E N M, Westerhuis J A, et al. Anal Chim Acta, 2003, 498(1/2): 133
12. [12]
  [12] Eilers P H C. Anal Chem, 2004, 76(2): 404
13. [13]
  [13] Fischer B, Grossmann J, Roth V, et al. Bioinformatics, 2006, 22(14): e132
14. [14]
  [14] Tsai T H, Tadesse M G, Di Poto C, et al. Bioinformatics, 2013, 29(21): 2774
15. [15]
  [15] Lin H, He L, Ma B. Bioinformatics, 2013, 29 (14): 1768
16. [16]
  [16] Christin C, Smilde A K, Hoefsloot H C J, et al. Anal Chem, 2008, 80(18): 7012
17. [17]
  [17] Christin C, Hoefsloot H C J, Smilde A K, et al. J Proteome Res, 2010, 9(3): 1483
18. [18]
  [18] Rost H, Malmstrom L, Aebersold R. Mol Cell Proteomics, 2012, 11(8): 540
19. [19]
  [19] Escher C, Reiter L, MacLean B, et al. Proteomics, 2012, 12(8): 1111
20. [20]
  [20] Old W M, Meyer-Arendt K, Aveline-Wolf L, et al. Mol Cell Proteomics, 2005, 4(10): 1487
21. [21]
  [21] Asara J M, Christofk H R, Freimark L M, et al. Proteomics, 2008, 8(5): 994
1. [1]
  Yanhui Zhong , Ran Wang , Zian Lin . Analysis of Halogenated Quinone Compounds in Environmental Water by Dispersive Solid-Phase Extraction with Liquid Chromatography-Triple Quadrupole Mass Spectrometry. University Chemistry, 2024, 39(11): 296-303. doi: 10.12461/PKU.DXHX202402017
2. [2]
  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
3. [3]
  Zunxiang Zeng , Yuling Hu , Yufei Hu , Hua Xiao . Analysis of Plant Essential Oils by Supercritical CO₂Extraction with Gas Chromatography-Mass Spectrometry: An Instrumental Analysis Comprehensive Experiment Teaching Reform. University Chemistry, 2024, 39(3): 274-282. doi: 10.3866/PKU.DXHX202309069
4. [4]
  Zian Lin , Yingxue Jin . Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS) for Disease Marker Screening and Identification: A Comprehensive Experiment Teaching Reform in Instrumental Analysis. University Chemistry, 2024, 39(11): 327-334. doi: 10.12461/PKU.DXHX202403066
5. [5]
  Chongjing Liu , Yujian Xia , Pengjun Zhang , Shiqiang Wei , Dengfeng Cao , Beibei Sheng , Yongheng Chu , Shuangming Chen , Li Song , Xiaosong Liu . Understanding Solid-Gas and Solid-Liquid Interfaces through Near Ambient Pressure X-Ray Photoelectron Spectroscopy. Acta Physico-Chimica Sinica, 2025, 41(2): 100013-. doi: 10.3866/PKU.WHXB202309036
6. [6]
  Hao Wu , Zhen Liu , Dachang Bai . ¹H NMR Spectrum of Amide Compounds. University Chemistry, 2024, 39(3): 231-238. doi: 10.3866/PKU.DXHX202309020
7. [7]
  Mingyang Men , Jinghua Wu , Gaozhan Liu , Jing Zhang , Nini Zhang , Xiayin Yao . 液相法制备硫化物固体电解质及其在全固态锂电池中的应用. Acta Physico-Chimica Sinica, 2025, 41(1): 2309019-. doi: 10.3866/PKU.WHXB202309019
8. [8]
  Zhuoming Liang , Ming Chen , Zhiwen Zheng , Kai Chen . Multidimensional Studies on Ketone-Enol Tautomerism of 1,3-Diketones By ¹H NMR. University Chemistry, 2024, 39(7): 361-367. doi: 10.3866/PKU.DXHX202311029
9. [9]
  Lingbang Qiu , Jiangmin Jiang , Libo Wang , Lang Bai , Fei Zhou , Gaoyu Zhou , Quanchao Zhuang , Yanhua Cui . 原位电化学阻抗谱监测长寿命热电池Nb₁₂WO₃₃正极材料的高温双放电机制. Acta Physico-Chimica Sinica, 2025, 41(5): 100040-. doi: 10.1016/j.actphy.2024.100040
10. [10]
  Jingming Li , Bowen Ding , Nan Li , Nurgul . Application of Comparative Teaching Method in Experimental Project Design of Instrumental Analysis Course: A Case Study in Chromatography Experiment Teaching. University Chemistry, 2024, 39(8): 263-269. doi: 10.3866/PKU.DXHX202312078
11. [11]
  Wei Huang , Weiwei Chen , Yongxing Tang . Green Mountains and Blue Waters Spanning Nine Centuries: Decrypting “The Picture of a Thousand Miles of Rivers and Mountains” from a Chemical Perspective. University Chemistry, 2024, 39(9): 189-195. doi: 10.12461/PKU.DXHX202312075
12. [12]
  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
13. [13]
  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
14. [14]
  Chenye An , Abiduweili Sikandaier , Xue Guo , Yukun Zhu , Hua Tang , Dongjiang Yang . 红磷纳米颗粒嵌入花状CeO₂分级S型异质结高效光催化产氢. Acta Physico-Chimica Sinica, 2024, 40(11): 2405019-. doi: 10.3866/PKU.WHXB202405019
15. [15]
  Yutong Dong , Huiling Xu , Yucheng Zhao , Zexin Zhang , Ying Wang . The Hidden World of Surface Tension and Droplets. University Chemistry, 2024, 39(6): 357-365. doi: 10.3866/PKU.DXHX202312022
16. [16]
  Gaoyan Chen , Chaoyue Wang , Juanjuan Gao , Junke Wang , Yingxiao Zong , Kin Shing Chan . Heart to Heart: Exploring Cardiac CT. University Chemistry, 2024, 39(9): 146-150. doi: 10.12461/PKU.DXHX202402011
17. [17]
  Zhuomin Zhang , Hanbing Huang , Liangqiu Lin , Jingsong Liu , Gongke Li . Course Construction of Instrumental Analysis Experiment: Surface-Enhanced Raman Spectroscopy for Rapid Detection of Edible Pigments. University Chemistry, 2024, 39(2): 133-139. doi: 10.3866/PKU.DXHX202308034
18. [18]
  Zhenli Sun , Ning Wang , Kexin Lin , Qin Dai , Yufei Zhou , Dandan Cao , Yanfeng Dang . Visual Analysis of Hotspots and Development Trends in Analytical Chemistry Education Reform. University Chemistry, 2024, 39(11): 57-64. doi: 10.12461/PKU.DXHX202403095
19. [19]
  Zhaoyang Li , Haiyan Zhao , Yali Zhang , Yuan Zhang , Shiqiang Cui . Integration of Nobel Prize Achievements in Analytical Technology with College Instrumental Analysis Course. University Chemistry, 2025, 40(3): 269-276. doi: 10.12461/PKU.DXHX202405131
20. [20]
  Zhening Lou , Quanxing Mao , Xiaogeng Feng , Lei Zhang , Xu Xu , Yuyang Zhang , Xueyan Liu , Hongling Kang , Dongyang Feng , Yongku Li . Practice of Implementing Blended Teaching in Shared Analytical Chemistry Course. University Chemistry, 2024, 39(2): 263-269. doi: 10.3866/PKU.DXHX202308089

Get Citation

PDF

XML

Metrics

PDF Downloads(0)
Abstract views(345)
HTML views(72)

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