A novel method to isolate protein N-terminal peptides from proteome samples using sulfydryl tagging and gold-nanoparticle-based depletion

详细信息    查看全文

• 作者：Lanting Li ; Runqing Wu ; Guoquan Yan ; Mingxia Gao…
• 关键词：N ; Termini ; Traut’s reagent ; Proteomics ; Posttranslational modification ; Gold nanoparticle
• 刊名：Analytical and Bioanalytical Chemistry
• 出版年：2016
• 出版时间：January 2016
• 年：2016
• 卷：408
• 期：2
• 页码：441-448
• 全文大小：1,262 KB
• 参考文献：1.Fortelny N, Yang S, Pavlidis P, Lange PF, Overall CM (2015) Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events. Nucleic Acids Res 43:D290–D297CrossRef
  2.Brown JL, Roberts WK (1976) Evidence that approximately 80 percent of soluble-proteins from Ehrlich ascites cells are Nalpha-acetylated. J Biol Chem 251(4):1009–1014
  3.Dormeyer W, Mohammed S, van Breukelen B, Krijgsveld J, Heck AJR (2007) Targeted analysis of protein termini. J Proteome Res 6(12):4634–4645CrossRef
  4.Doucet A, Butler GS, Rodriguez D, Prudova A, Overall CM (2008) Metadegradomics toward in vivo quantitative degradomics of proteolytic post-translational modifications of the cancer proteome. Mol Cell Proteomics 7(10):1925–1951CrossRef
  5.Kleifeld O, Doucet A, Keller UAD, Prudova A, Schilling O, Kainthan RK, Starr AE, Foster LJ, Kizhakkedathu JN, Overall CM (2010) Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products. Nat Biotechnol 28(3):281–288CrossRef
  6.Mahrus S, Trinidad JC, Barkan DT, Sali A, Burlingame AL, Wells JA (2008) Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell 134(5):866–876CrossRef
  7.Xu GQ, Shin SBY, Jaffrey SR (2009) Global profiling of protease cleavage sites by chemoselective labeling of protein N-termini. Proc Natl Acad Sci U S A 106(46):19310–19315CrossRef
  8.Wildes D, Wells JA (2010) Sampling the N-terminal proteome of human blood. Proc Natl Acad Sci U S A 107(10):4561–4566CrossRef
  9.Agard NJ, Maltby D, Wells JA (2010) Inflammatory stimuli regulate caspase substrate profiles. Mol Cell Proteomics 9(5):880–893CrossRef
  10.Timmer JC, Enoksson M, Wildfang E, Zhu W, Igarashi Y, Denault JB, Ma Y, Dummitt B, Chang YH, Mast AE, Eroshkin A, Smith JW, Tao WA, Salvesen GS (2007) Profiling constitutive proteolytic events in vivo. Biochem J 407:41–48CrossRef
  11.Bland C, Bellanger L, Armengaud J (2014) Magnetic immunoaffinity enrichment for selective capture and MS/MS analysis of N-terminal-TMPP-labeled peptides. J Proteome Res 13(2):668–680CrossRef
  12.Kim JS, Dai ZY, Aryal UK, Moore RJ, Camp DG, Baker SE, Smith RD, Qian WJ (2013) Resin-assisted enrichment of N-terminal peptides for characterizing proteolytic processing. Anal Chem 85(14):6826–6832CrossRef
  13.Timmer JC, Zhu WH, Pop C, Regan T, Snipas SJ, Eroshkin AM, Riedl SJ, Salvesen GS (2009) Structural and kinetic determinants of protease substrates. Nat Struct Mol Biol 16(10):1101–1108CrossRef
  14.Zhang XM, Ye JY, Engholm-Keller K, Hojrup P (2011) A proteome-scale study on in vivo protein N-alpha-acetylation using an optimized method. Proteomics 11(1):81–93CrossRef
  15.Sonomura K, Kuyama H, Matsuo E, Tsunasawa S, Nishimura O (2009) A method for terminus proteomics: selective isolation and labeling of N-terminal peptide from protein through transamination reaction. Bioorg Med Chem Lett 19(23):6544–6547CrossRef
  16.Zhao L, Zhang Y, Wei J, Cao D, Liu K, Qian X (2009) A rapid isolation and identification method for blocked N-terminal peptides by isothiocyanate-coupled magnetic nanoparticles and MS. Proteomics 9(18):4416–4420CrossRef
  17.Li LT, Yan GQ, Zhang XM (2015) Isolation of acetylated and free N-terminal peptides from proteomic samples based on tresyl-functionalized microspheres. Talanta 144:122–128CrossRef
  18.Shi Y, Meng JR, Deng CH (2012) Enrichment and detection of small molecules using magnetic graphene as an adsorbent and a novel matrix of MALDI-TOF-MS. Chem Commun 48(18):2418–2420CrossRef
  19.Zhang XY, Zhu SC, Deng CH, Zhang XM (2012) Highly sensitive thrombin detection by matrix assisted laser desorption ionization-time of flight mass spectrometry with aptamer functionalized core-shell Fe3O4@C@Au magnetic microspheres. Talanta 88:295–302CrossRef
  20.Xiong Y, Deng CH, Zhang XM (2014) Development of aptamer-conjugated magnetic graphene/gold nanoparticle hybrid nanocomposites for specific enrichment and rapid analysis of thrombin by MALDI-TOF MS. Talanta 129:282–289CrossRef
  21.Sato N, Tajima N (2012) Statistics of N-terminal alignment as a guide for refining prokaryotic gene annotation. Genomics 99(3):138–143CrossRef
  22.Aivaliotis M, Gevaert K, Falb M, Tebbe A, Konstantinidis K, Bisle B, Klein C, Martens L, Staes A, Timmerman E, Van Damme J, Siedler F, Pfeiffer F, Vandekerckhove J, Oesterhelt D (2007) Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis. J Proteome Res 6(6):2195–2204CrossRef
  23.Chen SH, Chen CR, Li DT, Hsu JL (2013) Improved N-alpha-acetylated peptide enrichment following dimethyl labeling and SCX. J Proteome Res 12(7):3277–3287CrossRef
  
• 作者单位：Lanting Li (1) (2)
  Runqing Wu (1) (2)
  Guoquan Yan (1) (2)
  Mingxia Gao (1) (2)
  Chunhui Deng (1) (2)
  Xiangmin Zhang (1) (2)
  
  1. Department of Chemistry, Fudan University, Shanghai, 200433, China
  2. Institute of Biomedical Sciences, Fudan University, Shanghai, 200433, China
  
• 刊物类别：Chemistry and Materials Science
• 刊物主题：Chemistry
  Analytical Chemistry
  Food Science
  Inorganic Chemistry
  Physical Chemistry
  Monitoring, Environmental Analysis and Environmental Ecotoxicology
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1618-2650

文摘

A novel method to isolate global N-termini using sulfydryl tagging and gold-nanoparticle-based depletion (STagAu method) is presented. The N-terminal and lysine amino groups were first completely dimethylated at the protein level, after which the proteins were digested. The newly generated internal peptides were tagged with sulfydryl by Traut’s reagent through digested N-terminal amines in yields of 96 %. The resulting sulfydryl peptides were depleted through binding onto nano gold composite materials. The Au–S bond is stable and widely used in materials science. Nano gold composite materials showed nearly complete depletion of sulfydryl peptides. A set of the acetylated and dimethylated N-terminal peptides were analyzed by liquid chromatography–tandem mass spectrometry. This method was demonstrated to be an efficient N-terminus enrichment method because of the use of an effective derivatization reaction, in combination with robust and relative easy to implement Au–S coupling. We identified 632 N-terminal peptides from 386 proteins in a mouse liver sample. The STagAu approach presented is therefore a facile and efficient method for mass-spectrometry-based analysis of proteome N-termini or protease-generated cleavage products. Keywords N-Termini Traut’s reagent Proteomics Posttranslational modification Gold nanoparticle