JI Mei-chao, FU Bin, ZHANG Yang-jun. Recent Progress of Analytical Methods of Proteomics Based on Mass Spectrometry[J]. Journal of Chinese Mass Spectrometry Society, 2021, 42(5): 862-877. DOI: 10.7538/zpxb.2021.0091
Citation: JI Mei-chao, FU Bin, ZHANG Yang-jun. Recent Progress of Analytical Methods of Proteomics Based on Mass Spectrometry[J]. Journal of Chinese Mass Spectrometry Society, 2021, 42(5): 862-877. DOI: 10.7538/zpxb.2021.0091

Recent Progress of Analytical Methods of Proteomics Based on Mass Spectrometry

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  • Proteomics is widely used in biological, pharmaceutical and pathological areas as a hot research topic in the post-genome era. The research areas of proteomics mainly cover qualitative analysis, such as protein expression profiles, protein post-translational modifications, protein-protein interactions, single cell proteomes, as well as proteome relative and absolute quantitative analysis. Mass spectrometry is an essential tool in proteome researches because of its sensitivity, accuracy and high throughput. In this paper, the identification and quantitative methods of proteomics based on mass spectrometry were reviewed, and the development direction of proteomics in the future was also prospected.
  • [1]
    LANDER E S, LINTON L M, BIRREN B, NUSBAUM C, ZODY M C, BALDWIN J, DEVON K, DEWAR K, DOYLE M, FITZHUGH W. Initial sequencing and analysis of the human genome[J]. Nature, 2001, 15(409): 860-921.
    [2]
    WASINGER V C, CORDWELL S J, CERPAPOLGAK A, YAN J X, GOOLEY A A, WILKINS M R, DUNCAN M W, HARRIS R, WILLIAMS K L, HUMPHERYSMITH I. Progress with geneproduct mapping of the mollicutes: mycoplasma genitalium[J]. Electrophoresis, 1995, 16(7): 1090-1094.
    [3]
    李煌,李松,徐芸,陈扬熙. 蛋白质组学技术在细胞信号传递机制研究中的应用[J]. 国际口腔医学杂志,2005,32(5):344-346.
    LI Huang, LI Song, XU Yun, CHEN Yangxi. Application of proteomics technology in the research of cell signal transfer mechanism[J]. The International Journal of Stomatology, 2005, 32(5): 344-346(in Chinese).
    [4]
    PANDEY A, MANN M. Proteomics to study genes and genomes[J]. Nature, 2000, 405(6 788): 837-846.
    [5]
    KARAS M, BAHR U, GUEBMANN U. Matrixassisted laser desorption ionization mass spectrometry[J]. Mass Spectrometry Reviews, 1991, 10(5): 335357.
    [6]
    FENN J, MANN M, MENG C, WONG S F, WHITEHOUSE C M. Electrospray ionization for mass spectrometry of large biomolecules[J]. Science, 1989, 246(4 926): 64-71.
    [7]
    顾劲扬,励建安. 蛋白质组技术进展及其在心血管研究中的应用[J]. 中国临床康复,2005,9(31):198-200.
    GU Jinyang, LI Jian′an. Progress of proteome technology and its application in cardiovascular research[J]. Clinical Rehabilitation of China, 2005,9(31): 198-200(in Chinese).
    [8]
    何国荣,廖宝琦,彭文平,许邦弘,陈朝荣,王亦生. 质谱分析技术原理与应用[M]. 北京:科学出版社,2014.
    [9]
    BUDNIK B, LEVY E, HARMANGE G, SAVOV N. SCoPEMS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation[J]. Genome Biology, 2018, 19(1): 161.
    [10]
    应万涛,焦丽燕,钱小红. 生物质谱技术与蛋白质组学[J]. 生物技术通讯,2004(增刊2):113-116.
    YING Wantao, JIAO Liyan, QIAN Xiaohong. Mass spectrometry technology and proteomics[J]. Biotechnology Communications, 2004(Suppl.2): 113116(in Chinese).
    [11]
    陈明,应万涛,钱小红. 规模化蛋白质组表达谱的研究进展及其挑战[J]. 生命的化学,2007(1):20-23.
    CHEN Ming, YING Wantao, QIAN Xiaohong. Research progress of largescale proteome express spectrum and its challenge[J]. The Chemistry of the Life, 2007(1): 20-23(in Chinese).
    [12]
    陈曼,何开武,任晓虎,杨细飞,邢红霞. 帕金森病患者血浆蛋白质组学的初步分析及鉴定[J]. 新乡医学院学报,2018(5):378381.
    CHEN Man, HE Kaiwu, REN Xiaohu, YANG Xifei, XING Hongxia. Preliminary analysis and identification of plasma proteomics in patients with Parkinson's disease[J]. Journal of Xinxiang Medical College, 2018(5): 378-381(in Chinese).
    [13]
    李瑞阳,王云之,葛蕊,石文昊,丁琛. 肝细胞体外培养去分化过程中转录因子表达谱分析[J]. 生物工程学报,2018,34(2):294302.
    LI Ruiyang, WANG Yunzhi, GE Rui, SHI Wenhao, DING Chen. Analysis of transcription factor in dedifferentiation in vitro[J]. Journal of Bioengineering, 2018, 34(2): 294-302(in Chinese).
    [14]
    JIANG Y, SUN A, ZHAO Y, YING W T, SUN H C, YANG X R. Proteomics identifies new therapeutic targets of earlystage hepatocellular carcinoma[J]. Nature, 2019(567): 257-261.
    [15]
    POSTIC G, MARCOUX J, REYS V, ANDREANI J, BROUCK Y V, BOUSQUET M P. Probing protein interaction networks by combining MS-based proteomics and structural data integration[J]. Journal of Proteome Research, 2020, 19(7): 2807-2820.
    [16]
    ZHANG L, YANG Z, TROTTIER J, BARBIER O, WANG L. LncRNA MEG3 induces cholestatic liver injury by interaction with PTBP1 to facilitate Shp mRNA decay: MEG3/PTBP1 in bile acid metabolism[J]. Hepatology, 2016, 65(2): 1611-1647.
    [17]
    李敏,孟祥茂. 动态蛋白质网络的构建,分析及应用研究进展[J]. 计算机研究与发展,2017,54(6):154-172.
    LI Min, MENG Xiangmao. The construction of the dynamic protein network, progress in analysis and application research[J]. Computer Research and Development, 2017, 54(6): 154-172(in Chinese).
    [18]
    SAFARIALIGHIARLOO N, TAGHIZADEH M, TABATABAEI S M, SHAHSAVARI S, NAMAKI S, KHODAKARIM S, REZAEITAVIRANI M. Identification of new key genes for type 1 diabetes through construction and analysis of proteinprotein interaction networks based on blood and pancreatic islet transcriptomes[J]. Journal of Diabetes, 2017, 9(8): 764-777.
    [19]
    刘艳霞,李雨浓,傅若秋,高宁. 多柔比星对乳腺癌细胞核内丝切蛋白相互作用蛋白影响的比较蛋白质组学研究[J]. 第三军医大学学报,2017,39(6):522528.
    LIU Yanxia, LI Yunong, FU Ruoqiu, GAO Ning. Comparative proteomics of polyorbitins on breast cancre[J]. Journal of the Third Military Medical University, 2017, 39(6): 522-528(in Chinese).
    [20]
    MALOVANNAYA A, LANZ R B, JUNG S Y, BULYNKO Y, LE T N, CHAN D W, DING C, SHI Y, YUCER N, KRENCIUTE G, KIM B J, LI C, CHEN R, LI W, WANG Y, O’MALLEY B, QIN J. Analysis of the human endogenous coregulator complexome[J]. Cell, 2011, 145(5): 787-799.
    [21]
    王建. 蛋白质相互作用数据库[J]. 中国生物化学与分子生物学报,2017,33(8):760-767.
    WANG Jian. Protein interaction database[J]. Chinese Journal of Biochemistry and Molecular Biology, 2017, 33(8): 760767(in Chinese).
    [22]
    NECHAY M, KLEINER R E. Highthroughput approaches to profile RNAprotein interactions[J]. Current Opinion in Chemical Biology, 2019, 54: 3744.
    [23]
    CASTELLO A, FISCHER B, EICHELBAUM K, HOROS R, BECKMANN B M, STREIN C, DAVEY N E, HUMPHREYS D T, PREISS T, STEINMETZ L M. Insights into RNA biology from an atlas of mammalian mRNAbinding proteins[J]. Cell, 2012, 149(6): 1393-1406.
    [24]
    BALTZ A G, MUNSCHAUER M, SCHWANHUSSER B, VASILE A, MURAKAWA Y, SCHUELER M, YOUNGS N, PENFOLDBROWN D, DREW K, MILEK M, WYLER E, BONNEAU R, SELBACH M, DIETERICH C, LANDTHALER M. The mRNABound proteome and its global occupancy profile on proteincoding transcripts[J]. Molecular Cell, 2012, 46(5): 674-690.
    [25]
    HE C, SIDOLI S, WAMEFORDTHOMSON R, TATOMER D C, WILUSZ J E, GARCIA B A, BONASIO R. Highresolution mapping of RNAbinding regions in the nuclear proteome of embryonic stem cells[J]. Molecular Cell, 2016, 64(2): 416-430.
    [26]
    TRENDEL J, SCHWALZL T, HOROS R, PRAKASH A, BATEMAN A, HENTZE M W, KRIJGSVELD J. The human RNAbinding proteome and its dynamics during translational arrest[J]. Cell, 2019, 176(1/2): 1-13.
    [27]
    QUEIROZ R M L, SMITH T, VILLANUEVA E, MARTISOLANO M, MIE M, MARIAVITTORIA P, MIREA D M, RAMAKRISHNA M, HARVEY R F, DEZI V, THOMAS G H, WILLIS A E, LILLEY K S. Comprehensive quantitation of RNAprotein interactions in any organism using orthogonal organic phase separation (OOPS)[J]. Nature Biotechnology, 2019, 37(6): 169-178.
    [28]
    URDANETA E C, VIEIRAVIEIRA C H, HICK T, WESSELS H H, FIGINI D, MOSCHALL R, MEDENBACH J, OHLER U, GRANNEMAN S, SELBACH M, BECKMANN B B. Purification of crosslinked RNAprotein complexes by phenoltoluol extraction[J]. Nature Communications, 2019, 10(1): 990.
    [29]
    MONDAL M, LIAO R, GUO J. Highly multiplexed singlecell protein analysis[J]. ChemistryA European Journal, 2018, 24(28): 7 0837 091.
    [30]
    TSAI C F, ZHAO R, WILLIAMS S M, MOORE R J, SCHULTZ K, CHRISLER W B, PASATOLIC L, RODLAND K D, SMITH R D, SHI T, ZHU Y, LIU T. An improved boosting to amplify signal with isobaric labeling (iBASIL) strategy for precise quantitative singlecell proteomics[J]. Molecular & Cellular Proteomics, 2020, 19(5): 828-838.
    [31]
    COUVILLION S P, ZHU Y, NAGY G, ADKINS J N, ANSONG C, RENSLOW R S, PIEHOWSIK P, IBRAHIM Y M, KELLY R, METZ T O. New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells[J]. The Analyst, 2019, 144(3): 794-807.
    [32]
    谭忠林,余方. 郭国骥教授团队绘制了人类细胞图谱[J]. 浙江大学学报(医学版),2020,49(2):208.
    TAN Zhonglin, YU Fang. Professor Guoji's team drew human cell maps[J]. Journal of Zhejiang University (Medical Edition), 2020, 49(2): 208(in Chinese).
    [33]
    班琳. 高通量单细胞蛋白组学新方法研究[D]. 武汉:华中科技大学,2019.
    [34]
    ZHENG W, ZHANG X. Single cell proteomics for molecular targets in lung cancer: highdimensional data acquisition and analysis[J]. Advances in Experimental Medicine & Biology, 2018, 1068: 73-78.
    [35]
    LEI Y, ZHANG Z, LIU Y Z, GAO Y, GU J K. Recent advances in singlecell analysis by mass spectrometry[J]. The Analyst, 2018, 144(3): 824845.
    [36]
    HARRISON S, NIKOLAI S. Transformative opportunities for singlecell proteomics[J]. Journal of Proteome Research, 2018, 17(8): 2 5652 571.
    [37]
    LI Z Y, HUANG M, WANG X K, ZHU Y, LI J S, WONG C C, FANG Q. Nanoliterscale oilairdroplet chipbased single cell proteomic analysis[J]. Analytical Chemistry, 2018, 90(8): 5430-5438.
    [38]
    秦少杰,白玉,刘虎威. 基于质谱的单细胞蛋白质组学分析方法及应用[J]. 色谱,2021,39(2):142151.
    QIN Shaojie, BAI Yu, LIU Huwei. Analysis method and application of singlecell proteomics based on mass spectrometry[J]. Chromatogram, 2021, 39(2): 142151(in Chinese).
    [39]
    ZHANG L W, VERTES A. Singlecell mass spectrometry approaches to explore cellular heterogeneity[J]. Angewandte Chemie, 2018, 57(17): 4 4664 477.
    [40]
    MANN M, JENSEN O N. Proteomic analysis of posttranslational modifications[J]. Nature Biotechnology, 2003, 21(3): 255261.
    [41]
    HUMPHREI S J, OZGE K, JAMES D E, MANN M. Highthroughput and highsensitivity phosphoproteomics with the EasyPhos platform[J]. Nature Protocols, 2018, 13: 1897-1916.
    [42]
    杨倩,王丹,常丽丽,孙勇,靳翔,王旭初. 生物质谱技术研究进展及其在蛋白质组学中的应用[J]. 中国农学通报,2015,31(1):239246.
    YANG Qian, WANG Dan, CHANG Lili, SUN Yong, JIN Xiang, WANG Xuchu. Research progress of biomass spectrometry and its application in proteomics[J]. China Agricultural Bulletin, 2015, 31(1): 239-246(in Chinese).
    [43]
    李凯旋,徐锋,徐平. 酪氨酸磷酸化蛋白质组学技术研究进展及其在生物医学研究中的应用[J]. 生物工程学报,2021,37(1):100111.
    LI Kaixuan, XU Feng, XU Ping. Research progress of tyrosine phosphorylation proteomics technology and its application in biomedical research[J]. Chinese Journal of Biotechnology, 2021, 37(1): 100-111(in Chinese).
    [44]
    RILEY N M, COON J J. Phosphoproteomics in the age of rapid and deep proteome profiling[J]. Analytical Chemistry, 2016, 88(1): 7494.
    [45]
    STECHOW L V, FRANCAVILLA C, OLSEN J V. Recent findings and technological advances in phosphoproteomics for cells and tissues[J]. Expert Review of Proteomics, 2015, 12(5): 461-489.
    [46]
    毕炜,王京兰,钱小红,蔡耘. 磷酸化蛋白质组研究中的富集策略[J]. 生物技术通讯,2007,18(3):515518.
    BI Wei, WANG Jinglan, QIAN Xiaohong, CAI Yun. Enrichment strategies in the phosphorylation of proteomics studies[J]. Biotechnology Communications, 2007, 18(3): 515-518(in Chinese).
    [47]
    王银,徐平. 乳腺癌磷酸化蛋白质组学研究进展[J]. 中华乳腺病杂志(电子版),2020,14(1):5053.
    WANG Yin, XU Ping. Progress in phosphorylation proteomics of breast cancer[J]. Chinese Journal of Breast Diseases (Electronic Edition), 2020, 14(1): 5053(in Chinese).
    [48]
    李素贞,徐锋,徐平. 高转移肝癌细胞HCCLM6的酪氨酸磷酸化蛋白质组学研究[J]. 军事医学,2019,43(2):3035.
    LI Suzhen, XU Feng, XU Ping. Study on tyrosine phorylation proteomics of hcclm6 in high transstatic hepocellular cancer cells[J]. Military Medical Sciences, 2019, 43(2): 30-35(in Chinese).
    [49]
    DONG M, BIAN Y, WANG Y, DONG J, YAO Y T, DENG Z Z, QIN H Q, ZOU H F, YE M L. Sensitive, robust, and costeffective approach for tyrosine phosphoproteome analysis[J]. Analytical Chemistry, 2017, 89(17): 9307-9314.
    [50]
    MIAO M, YU F, WANG D, TONG Y J, YANG L T, XU J Y, QIU Y, ZHOU X, ZHAO X L. Proteomics profiling of host cell response via protein expression and phosphorylation upon dengue virus infection[J]. Virologica Sinica, 2019, 34(5): 549-562.
    [51]
    ZHAO X Y, ZHANG W J, LIU T, DONG H Y, HUANG J J, SUN C Q, WANG G S, QIAO X H, QIN W J. A fast sample processing strategy for largescale profiling of human urine phosphoproteome by mass spectrometry[J]. Talanta: The International Journal of Pure and Applied Analytical Chemistry, 2018, 185: 166-173.
    [52]
    SUN J, ZHANG W J, SHI Z M, QIN W J, QIAN X H. A Novel method for analysis of tyrosine thosphopeptides based on a centrifugal enrichment device[J]. Chinese Journal of Analytical Chemistry, 2017, 45(10): 1434-1440.
    [53]
    QIN W J, ZHANG W J, SONG L N, Zhang Y J, QIAN X H. Surface initiated atom transfer radical polymerization: access to three dimensional wavelike polymer structure modified capillary columns for online phosphopeptide enrichment[J]. Analytical Chemistry, 2010, 82(22): 9461-9468.
    [54]
    ZHANG Y, JING H, MENG B, QIAN X H, YING W T. LCysteine functionalized straticulate C3N4 for the selective enrichment of glycopeptides[J]. Journal of Chromatography A, 2019, 1 610: 460-545.
    [55]
    WANG L, ARYAL U K, DAI Z Y, MASON A C, MONROE M E, TIAN Z X, ZHOU J Y, SU D, WEITZ K K, LIU T, CAMP D G, SMITH R D, BAKER S E, QIAN W J. Mapping Nlinked glycosylation sites in the secretome and whole cells of Aspergillus niger using hydrazide chemistry and mass spectrometry[J]. Journal of Proteome Research, 2019, 11(1): 143-156.
    [56]
    邵文亚,梁玉,梁振,张丽华,张玉奎. N糖基化蛋白质组样品富集策略的研究进展[J]. 分析测试学报,2018,37(10):123127.
    SHAO Wenya, LIANG Yu, LIANG Zhen, ZHANG Lihua, ZHANG Yukui. Research advances of enrichment approaches in Nglycoproteomics[J]. Analytic Test Journal, 2018, 37(10): 123-127(in Chinese).
    [57]
    PAP A, TASNADI E, MEDZIHRADSZKY K F, DARRULA Z. Novel Olinked sialoglycan structures in human urinary glycoproteins[J]. Molecular Omics, 2020, 16: 156-164.
    [58]
    XIA C S, JIAO F L, GAO F Y, WANG H P, LV Y Y, SHEN Y H, ZHANG Y J, QIAN X H. Twodimensional MoS2based zwitterionic hydrophilic interaction liquid chromatography material for the specific enrichment of glycopeptides[J]. Analytical Chemistry, 2018, 90(11): 6651-6659.
    [59]
    HUO B B, CHEN M L, CHEN J J, LI Y Y, ZHANG W J, WANG J H, QIN W J, QIAN X H. A sequential separation strategy for facile isolation and comprehensive analysis of human urine Nglycoproteome[J]. Analytical and Bioanalytical Chemistry, 2018, 410: 7305-7312.
    [60]
    秦伟捷,张万军,刘彤,沈丙权,王建华,邓玉林,钱小红. OGlcNAc糖基化修饰蛋白质和肽段的富集鉴定新方法研究[C]. 第21届全国色谱学术报告会及仪器展览会会议论文集,2017:232.
    [61]
    黄怡,李晓宇,田芳,钱小红,应万涛. 质谱方法实现抗体类药物糖链修饰的鉴定与定量研究[J]. 中国生物工程杂志,2018,38(1):3241.
    HUANG Yi, LI Xiaoyu, TIAN Fang, QIAN Xiaohong, YING Wantao. Identification and quantification of antibody sugar chain modification by mass spectrometric method[J]. Chinese Journal of Bioengineering, 2018, 38(1): 32-41(in Chinese).
    [62]
    谭增琦,周岳,杨刚龙,李想,关峰. 凝集素辅助平分型GlcNAc糖基化蛋白质组学分析[J]. 农业生物技术学报,2017,25(1):7483.
    TAN Zengqi, ZHOU Yue, YANG Ganglong, LI Xiang, GUAN Feng. Analysis of proteomics of glcnac[J]. Journal of Agricultural Biotechnology, 2017, 25(1): 7483(in Chinese).
    [63]
    赵洋,张勇,王明超,孟波,应万涛,钱小红. 重组含糖识别结构域的人源半乳糖凝集素3在糖蛋白/糖肽富集中的应用[J]. 色谱,2018,36(12):1321.
    ZHAO Yang, ZHANG Yong, WANG Mingchao, MENG Bo, YING Wantao, QIAN Xiaohong. Application of human galactose contintin3 of recombinant sugar identification domain in glycoprotein/glycopeptide enrichment[J]. Chromatogram, 2018, 36(12): 13-21(in Chinese).
    [64]
    刘光宪,管珊红,王辉,冯健雄. CID/ETD质谱对糖基化多肽的分析[J]. 食品科学,2013,34(17):16.
    LIU Guangxian, GUAN Shanhong, WANG Hui, FENG Jianxiong. Analysis of glycosylated polypeptide by CID/ETD mass spectrometry[J]. Food Science, 2013, 34(17): 1-6(in Chinese).
    [65]
    张思琦. FOXA1在人乳腺癌细胞中的表达、纯化及OGlcNAc糖基化位点鉴定[C]. 第八届泛环渤海生物化学与分子生物学会2018年学术交流会论文集,2018.
    [66]
    STAVENHAGEN K, KAYILI H M, HOLST S, KOELEMAN C A M, ENGEL R, WOUTERS D, ZEERLEDER S, SALIH B, WUHRER M. N and Oglycosylation analysis of human C1inhibitor reveals extensive mucintype O-glycosy-lation[J]. Molecular & Cellular Proteomics, 2017, 17(6): 1 2251 338.
    [67]
    LAN Q Y, WANG Y H, SUN Z, LI Y C, ZHANG C, CHANG L, GAO Y, WU J Z, WANG F Q, XU P. Quantitative proteomics combined with two genetic strategies for screening substrates of ubiquitin ligase Hrt3[J]. Journal of Proteome Research, 2019, 19(1): 493-502.
    [68]
    XIAO W, LIU Z, LUO W, GAO Y, CHANG L, LI Y C, XU P. Specific and unbiased detection of polyubiquitination via a sensitive nonantibody approach[J]. Analytical Chemistry, 2019, 92(1): 1074-1080.
    [69]
    XIAO W D, ZHANG J L, WANG Y H, LIU Z J, WANG F Q, SUN J S, CHANG L, XIA Z P, LI Y C, XU P. AcLysargiNase complements trypsin for the identification of ubiquitinated sites[J]. Analytical Chemistry, 2019, 91(24): 15890-15898.
    [70]
    AKIMOV V, RIGBOFE K T G, NIELSEN M M, BLAGOEV B. Characterization of ubiquitination dependent dynamics in growth factor receptor signaling by quantitative proteomics[J]. Molecular Biosystems, 2011, 7(12): 3223-3233.
    [71]
    GAO Y, LI Y C, ZHANG C P, ZHAO M Z, DENG C, LAN Q Y, LIU Z X, SU N, WANG J W, XU F, XU Y R, PING L Y, CHANG L, GAO H Y, WU J Z, XUE Y, DENG Z X, PENG J M, XU P. Enhanced purification of ubiquitinated proteins by engineered tandem hybrid ubiquitinbinding domains (ThUBDs)[J]. Molecular & Cellular Proteomics, 2016, 15(4): 1381-1396.
    [72]
    HJERPE R, AILLET F, LOPITZOTSOA F, LANG V, ENGLAND P, RODRIGUEZ M S. Efficient protection and isolation of ubiquitylated proteins using tandem ubiquitibinding entities[J]. Embo Reports, 2009, 10(11): 1250.
    [73]
    MEDZIHRADSZKY K F, DARULA Z, PERLSON E, FAINZILBER M, CHALKLEY R J, BALL H, GREENBAUM D, BOGYO M, TYSON D R, BRADSHAW R A. OSulfonation of serine and threonine[J]. Journal of Biological Chemistry, 2015, 3: 429-443.
    [74]
    REDDIE K G, SEO Y H, III W, LEONARD S E, CARROLL K S. A chemical approach for detecting sulfenic acidmodified proteins in living cells[J]. Molecular Biosystems, 2008, 4(6): 521-531.
    [75]
    PAULSEN C E, TRUONG T H, GARCIA F J, HOMANN A, GUPTA V, LEONARD S E, CARROL K S. Peroxidedependent sulfenylation of the EGFR catalytic site enhances kinase activity[J]. Nature Chemical Biology, 2012, 8(1): 57-64.
    [76]
    YANG J, GUPTA V, CARROLL K S, LIEBLER D C. Sitespecific mapping and quantification of protein Ssulphenylation in cells[J]. Nature Communications, 2017, 5(4 776): 187-207.
    [77]
    GUPTA V, YANG J, LEIBLER D C, CAROLL K S. Diverse redoxome reactivity profiles of carbon nucleophiles[J]. J Am Chem Soc, 2017, 139(15): 5588-5595.
    [78]
    FU L, LIU K, FERRIERA R B, CARROLL K S, YANG J. Proteomewide analysis of cysteine Ssulfenylation using a benzothiazinebased probe[J]. Current Protocols in Protein Science, 2019, 95(1): 1-20.
    [79]
    赵丽艳,周春喜,张养军,蔡耘,钱小红. 基于生物质谱技术的磺酸化修饰策略及其在蛋白质组学中的应用[J]. 质谱学报,2007,28(3):185-192.
    ZHAO Liyan, ZHOU Chunxi, ZHANG Yangjun, CAI Yun, QIAN Xiaohong. Modification strategy based on biomass spectroscopy and its application in proteomics[J]. Journal of Chinese Mass Spectroscopy Society, 2007, 28(3): 185-192(in Chinese).
    [80]
    MIKESH L M, UEBERHEIDE B, CHI A, COON J J, SYKA J E P, SHABANOWITZ J, HUNT D F. The utility of ETD mass spectrometry in proteomic analysis[J]. BBAProteins and Proteomics, 2006, 1 764(12): 1811-1822.
    [81]
    SEIBERT C, SAKMAR T P. Toward a framework for sulfoproteomics: synthesis and characterization of sulfotyrosinecontaining peptides[J]. Peptide Science, 2008, 90(3): 459-477.
    [82]
    牟永莹,顾培明,马博,闫文秀,王道平,潘映红. 基于质谱的定量蛋白质组学技术发展现状[J]. 生物技术通报,2017,33(9):73-84.
    MU Yongying, GU Peiming, MA Bo, YAN Wenxiu, WANG Daoping, PAN Yinghong. Development status of quantitative proteomics technology based on mass spectrometry[J]. Biotechnology Bulletin, 2017, 33(9): 73-84(in Chinese).
    [83]
    曹冬,张养军,钱小红. 基于生物质谱的蛋白质组学绝对定量方法研究进展[J]. 质谱学报,2008,29(3):185191.
    CAO Dong, ZHANG Yangjun, QIAN Xiaohong. Research progress in absolute quantitative methods of proteomics based on biomass spectrometry[J]. Journal of Mass Spectroscopy, 2008, 29(3): 185-191(in Chinese).
    [84]
    常乘,朱云平. 基于质谱的定量蛋白质组学策略和方法研究进展[J]. 中国科学:生命科学,2015,45(5):922.
    CHANG Cheng, ZHU Yunping. Research progress on the strategy and methods of quantitative proteomics based on mass spectrometry[J]. Chinese Science: Life Sciences, 2015, 45(5): 9-22(in Chinese).
    [85]
    BINDSCHEDLER L V, CRAMER R. Quantitative plant proteomics[J]. Proteomics, 2011, 11(4): 756775.
    [86]
    XIONG X G, LIANG Q H, ZHANG C H, YANG W, WEI H, PENG W, ZHE W, XIA Z A. Serum proteome alterations in patients with cognitive impairment after traumatic brain injury revealed by iTRAQbased quantitative proteomics[J]. Biomed Research International, 2017(2): 1-13.
    [87]
    DU C Q, WENG Y Z, LOU J J, ZENG G Z, LIU X W, JIN H F, LIN S N, TANG L J. Isobaric tags for relative and absolute quantitationbased proteomics reveals potential novel biomarkers for the early diagnosis of acute myocardial infarction within 3 h[J]. International Journal of Molecular Medicine, 2019, 43(5): 1991-2004.
    [88]
    REN H Y, LUO M X, CHEN J Z, ZHOU Y M, LI X M, ZHAN Y Y, SHEN D Y, CHEN B. Identification of TPD52 and DNAJB1 as two novel bile biomarkers for cholangiocarcinoma by iTRAQbased quantitative proteomics analysis[J]. Oncology Reports, 2019, 42(6): 2622-2634.
    [89]
    TANG P X, TAO L Y, YUAN C H, ZHANG L F, XIU D R. Serum derived exosomes from pancreatic cancer patients promoted metastasis: an iTRAQbased proteomic analysis[J]. OncoTargets and Therapy, 2019, 12: 9329-9339.
    [90]
    ZHOU Q, XIE F, ZHOU B, WANG J, WU B, LI L, KANG Y, DAI R, JIANG Y. Differentially expressed proteins identified by TMT proteomics analysis in bone marrow microenvironment of osteoporotic patients[J]. Osteoporosis International, 2019, 30: 1089-1098.
    [91]
    HOU C Y, GUO D Q, YU X, WANG S Y, LIU T H. TMTbased proteomics analysis of the antihepatocellular carcinoma effect of combined dihydroartemisinin and sorafenib[J]. Biomedicine & Pharmacotherapy, 2020, 126: 109 862.
    [92]
    ONG S E, BLAGOEV B, KRATCHMAROVA L, KRISTENSEN D B, STEEN H, MANN M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics[J]. Molecular & Cellular Proteomics, 2002, 1(5): 376-386.
    [93]
    NEUBERT T A, TEMPST P. SuperSILAC for tumors and tissues[J]. Nature Methods, 2010, 7(5): 361362.
    [94]
    HEBERT A S, MERRILL A E, BAILEY D J, STILL A J, WESTPHALL M S, STREITER E R, PAGLIARINI D J, COON J J. Neutronencoded mass signatures for multiplexed proteome quantification[J]. Nature Methods, 2013, 10(4): 332-334.
    [95]
    武鹏,贺福初,姜颖. 定量蛋白质组学无标记定量方法的研究进展[J]. 生物化学与生物物理进展,2013,40(3):281292.
    WU Peng, HE Fuchu, JIANG Ying. Research progress of unlabeled quantitative methods in quantitative proteomics[J]. Biochemistry and Ophysical Advances, 2013, 40(3): 281-292(in Chinese).
    [96]
    PIERSMAR S R, FIEDLER U, SPAN S, LINGNAU A, PHAM T V, HOFFMANN S, KUBBUTAT M H G, JIMENEZ C R. Workflow comparison for labelfree, quantitative secretome proteomics for cancer biomarker discovery: method evaluation, differential analysis, and verification in serum[J]. Journal of Proteome Research, 2010, 9(4): 1 913.
    [97]
    GRIFFIN N M, YU J, LONG F, OH P, SHORE S, LI Y, KOZIOL J A, SCHNITZER J E. Labelfree, normalized quantification of complex mass spectrometry data for proteomic analysis[J]. Nature Biotechnology, 2010, 28(1): 83-89.
    [98]
    ASARA J M, CHRISTOFK H R, FREIMARK L M, CANTLEY L C. A labelfree quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen[J]. Proteomics, 2010, 8(5): 994-999.
    [99]
    CHELIUS D, BONDARENKO P V. Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry[J]. Journal of Proteome Research, 2002, 1(4): 317.
    [100]
    NAKAMURA T, DOHMAE N, TAKIO K. Characterization of a digested protein complex with quantitative aspects: an approach based on accurate mass chromatographic analysis with Fourier transformion cyclotron resonance mass spectrometry[J]. Proteomics, 2010, 4(9): 2558-2566.
    [101]
    SILVA J C, GORENSTEIN M V, LI G Z, VISSERS J P C, GEROMANOS S J. Absolute quantification of proteins by LCMSE a virtue of parallel ms acquisition[J]. Molecular & Cellular Proteomics, 2006, 5(1): 144-156.
    [102]
    GROSSMANN J, ROSCHITZKI B, PANSE C, FORES C, BARKOWOESTERRRICHER S, SCHLAPBACH R. Implementation and evaluation of relative and absolute quantification in shotgun proteomics with labelfree methods[J]. Journal of Proteomics, 2010, 73(9): 1740-1746.
    [103]
    SCHUBERT O T, ROST H L, COLLINS B C, ROSENBERGER G, AEBERSOLD R. Quantitative proteomics: challenges and opportunities in basic and applied research[J]. Nature Protocols, 2017, 12(7): 1289-1294.
    [104]
    GUAN S H, TAYLOR P P, HAN Z W, MORAN M F, MA B. DDIA: data dependentindependent acquisition proteomicsDDA and DIA in a single LC-MS/MS run[J]. Biorxiv, 2019, doi: 10.1101/802231.
    [105]
    张惠萍,刘泰驿. 一种基于LCMS的细胞外泌体脂质组学分析方法:中国,CN111351879A[P]. 2020.
    [106]
    HARLAN R, ZHANG H. Targeted proteomics: a bridge between discovery and validation[J]. Expert Rev Proteomics, 2014, 11(6): 657-661.
    [107]
    GERBER S A, RUSH J, STEMMAN O, KIRSCHNER M W, GYGI S P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS[J]. Proceedings of the National Academy of Sciences, 2003, 100(12): 6940-6945.
    [108]
    AWASTHI S, MAITY T, OYLER B L, ZHANG X, GOODLETT D R, GUHA U. Dataset describing the development, optimization and application of SRM/MRM based targeted proteomics strategy for quantification of potential biomarkers of EGFR TKI sensitivity[J]. Data in Brief, 2018, 19: 424-436.
    [109]
    HUANG H, TONG T T, YAU L F, WANG J R, LAI M H, ZHANG C R, WEN X H, LI S N, LI K Y, LIU J Q, MA H X, TSANG B K, JIANG Z H. Chemerin isoform analysis in human biofluids using an LC/MRMMSbased targeted proteomics approach with stable isotope-labeled standard[J]. Analytica Chimica Acta, 2020, 1139: 79-87.
    [110]
    GALLIEN S, DOMON B. Detection and quantification of proteins in clinical samples using high resolution mass spectrometry[J]. Methods, 2015, 81: 15-23.
    [111]
    SWEREDOSKI M J, MORADIAN A, HESS S. Highresolution parallel reaction monitoring with electron transfer dissociation for middledown proteomics: an application to study the quantitative changes induced by histone modifying enzyme inhibitors and activators[J]. Methods Mol Biol, 2017, 1 647: 61-69.
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