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An Overview of The Phosphoproteomic Workflow

Yıl 2018, Cilt: 8 Sayı: 1, 23 - 32, 30.04.2018

Öz

Proteomic studies permit the evaluation of pathological or physiological events in more detail through technological developments in the fields of mass spectrometry and chromatography. Protein phosphorylation, an important research area of mass spectrometry-based proteomic studies, plays an active role as a dynamic marker of molecular activity in the pathological alteration of cellular processes. Therefore, phosphoproteomic studies are gaining importance in the elucidation of molecular mechanisms of diseases and the development of effective diagnostic and treatment methods. Identification and quantitative analysis of phosphoproteins requires the use of highly efficient and reproducible methods. The development of existing methods is ongoing in order to maximize the efficiency of phosphoproteomic applications. We hope that this study, which explains the basic methodology of mass spectrometry-based phosphoproteomic research and discusses its practical challenges, will be useful for researchers interested in MS-based phosphoproteomics.

Kaynakça

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  • Caprioli RM, Farmer TB, Gile J. Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS. Anal Chem. 1997;69(23):4751-60.
  • Carruthers NJ, Rosenspire AJ, Caruso JA, Stemmer PM. Low level Hg(2+) exposure mo-dulates the B-cell cytoskeletal phosphoproteome. J Proteomics. 2018;173:107-114.
  • Carson RH, Lewis CR, Erickson MN, Zagieboylo AP, Naylor BC, Li KW, Farnsworth PB, Price JC. Imaging regiospecific lipid turnover in mouse brain with desorption elect-rospray ionization mass spectrometry. J Lipid Res. 2017;58(9):1884-1892.
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Fosfoproteomik Uygulama Basamaklarına Genel Bakış

Yıl 2018, Cilt: 8 Sayı: 1, 23 - 32, 30.04.2018

Öz

Proteomik çalışmalar, kütle spektrometresi ve kromatografi alanındaki teknolojik gelişmeler sayesinde patolojik ya da fizyolojik olayları daha detaylı olarak değerlendirebilmemize imkan sağlamaktadır. Kütle spektrometresi tabanlı proteomik çalışmaların önemli bir araştırma alanı olan protein fosforilasyonları, hücresel işleyişin patolojik değişiminde moleküler aktivitenin dinamik belirteçleri olarak etkin rol oynar. Bu nedenle hastalıkların moleküler mekanizmalarının aydınlatılmasında ve etkin tanı-tedavi yöntemlerinin geliştirilmesinde fosfoproteomik çalışmalar artan öneme sahiptir. Fosfoproteinlerin tanımlanması ve miktar analizlerinin yapılabilmesi oldukça verimli tekrarlanabilir yöntemlerin kullanılmasını gerektirir. Bu amaçla fosfoproteomik uygulamalardaki verimliliğin en üst düzeye çıkarılmasında mevcut yöntemler geliştirilmeye devam etmektedir. Kütle spektrometresi tabanlı fosfoproteomik araştırmaların temel metodolojisinin anlatıldığı ve uygulamalarda karşılaşılan zorlukların tartışıldığı bu çalışmanın, MS tabanlı fosfoproteomik alanına ilgi duyan araştırmacılara yardımcı olacağını umuyoruz.

Kaynakça

  • Abdallah C, Dumas-Gaudot E, Renaut J, Sergeant K. Gel-based and gel-free quantitative proteomics approaches at a glance. Int J Plant Genomics. 2012;2012:494572.
  • Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature. 2003;422(6928):198-207.
  • Aebersold R, Mann M. Mass-spectrometric exploration of proteome structure and func-tion. Nature. 2016 Sep 15;537(7620):347-55.
  • Aryal UK, Ross AR. Enrichment and analysis of phosphopeptides under different expe-rimental conditions using titanium dioxide affinity chromatography and mass spectro-metry. Rapid Commun Mass Spectrom. 2010;24(2):219-31.
  • Bantscheff M, Lemeer S, Savitski MM, Kuster B. Quantitative mass spectrometry in pro-teomics: critical review update from 2007 to the present. Anal Bioanal Chem. 2012;404(4):939-65.
  • Batth TS, Olsen JV. Offline High pH Reversed-Phase Peptide Fractionation for Deep Phosphoproteome Coverage. Methods Mol Biol. 2016;1355:179-92.
  • Beltran L, Cutillas PR. Advances in phosphopeptide enrichment techniques for phosphop-roteomics. Amino Acids. 2012;43(3):1009-24.
  • Blacken GR, Volný M, Diener M, Jackson KE, Ranjitkar P, Maly DJ, Turecek F. Reactive landing of gas-phase ions as a tool for the fabrication of metal oxide surfaces for in situ phosphopeptide enrichment. J Am Soc Mass Spectrom. 2009;20(6):915-26.
  • Boersema PJ, Foong LY, Ding VM, Lemeer S, van Breukelen B, Philp R, Boekhorst J, Snel B, den Hertog J, Choo AB, Heck AJ. In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity puri-fication and stable isotope dimethyl labeling. Mol Cell Proteomics. 2010;9(1):84-99.
  • Boersema PJ, Mohammed S, Heck AJ. Hydrophilic interaction liquid chromatography (HILIC) in proteomics. Anal Bioanal Chem. 2008;391(1):151-9.
  • Caprioli RM, Farmer TB, Gile J. Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS. Anal Chem. 1997;69(23):4751-60.
  • Carruthers NJ, Rosenspire AJ, Caruso JA, Stemmer PM. Low level Hg(2+) exposure mo-dulates the B-cell cytoskeletal phosphoproteome. J Proteomics. 2018;173:107-114.
  • Carson RH, Lewis CR, Erickson MN, Zagieboylo AP, Naylor BC, Li KW, Farnsworth PB, Price JC. Imaging regiospecific lipid turnover in mouse brain with desorption elect-rospray ionization mass spectrometry. J Lipid Res. 2017;58(9):1884-1892.
  • Chen H, Talaty NN, Takáts Z, Cooks RG. Desorption electrospray ionization mass spect-rometry for high-throughput analysis of pharmaceutical samples in the ambient environ-ment. Anal Chem. 2005;77(21):6915-27.
  • Chen SY, Juang YM, Chien MW, Li KI, Yu CS, Lai CC. Magnetic iron oxide nanopartic-le enrichment of phosphopeptides on a radiate microstructure MALDI chip. Analyst. 2011;136(21):4454-9.
  • Chen X, Wei S, Ji Y, Guo X, Yang F. Quantitative proteomics using SILAC: Principles, applications, and developments. Proteomics. 2015;15(18):3175-92.
  • Choudhary C, Mann M. Decoding signalling networks by mass spectrometry-based prote-omics. Nat Rev Mol Cell Biol. 2010;11(6):427-39.
  • Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Sha-movsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P. The Reactome pathway knowledgebase. Nucleic Acids Res. 2014;42 (Database issue):D472-7.
  • de Hoog CL, Mann M. Proteomics. Annu Rev Genomics Hum Genet. 2004;5:267-93. Drabovich Andrei P., et al. "Proteomic and mass spectrometry technologies for biomarker discovery." Proteomic and metabolomic approaches to biomarker discovery 2013; 17-37.
  • Dunn JD, Reid GE, Bruening ML. Techniques for phosphopeptide enrichment prior to analysis by mass spectrometry. Mass Spectrom Rev. 2010 Jan-Feb;29(1):29-54.
  • Dyballa N, Metzger S. Fast and sensitive coomassie staining in quantitative proteomics. Methods Mol Biol. 2012;893:47-59.
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Toplam 96 adet kaynakça vardır.

Ayrıntılar

Birincil Dil Türkçe
Konular Sağlık Kurumları Yönetimi
Bölüm Makale
Yazarlar

Mustafa Gani Sürmen 0000-0001-9084-7528

Saime Sürmen Bu kişi benim

Sadrettin Pençe Bu kişi benim

Yayımlanma Tarihi 30 Nisan 2018
Yayımlandığı Sayı Yıl 2018 Cilt: 8 Sayı: 1

Kaynak Göster

APA Sürmen, M. G., Sürmen, S., & Pençe, S. (2018). Fosfoproteomik Uygulama Basamaklarına Genel Bakış. Deneysel Tıp Araştırma Enstitüsü Dergisi, 8(1), 23-32.
AMA Sürmen MG, Sürmen S, Pençe S. Fosfoproteomik Uygulama Basamaklarına Genel Bakış. Deneysel Tıp Araştırma Enstitüsü Dergisi. Nisan 2018;8(1):23-32.
Chicago Sürmen, Mustafa Gani, Saime Sürmen, ve Sadrettin Pençe. “Fosfoproteomik Uygulama Basamaklarına Genel Bakış”. Deneysel Tıp Araştırma Enstitüsü Dergisi 8, sy. 1 (Nisan 2018): 23-32.
EndNote Sürmen MG, Sürmen S, Pençe S (01 Nisan 2018) Fosfoproteomik Uygulama Basamaklarına Genel Bakış. Deneysel Tıp Araştırma Enstitüsü Dergisi 8 1 23–32.
IEEE M. G. Sürmen, S. Sürmen, ve S. Pençe, “Fosfoproteomik Uygulama Basamaklarına Genel Bakış”, Deneysel Tıp Araştırma Enstitüsü Dergisi, c. 8, sy. 1, ss. 23–32, 2018.
ISNAD Sürmen, Mustafa Gani vd. “Fosfoproteomik Uygulama Basamaklarına Genel Bakış”. Deneysel Tıp Araştırma Enstitüsü Dergisi 8/1 (Nisan 2018), 23-32.
JAMA Sürmen MG, Sürmen S, Pençe S. Fosfoproteomik Uygulama Basamaklarına Genel Bakış. Deneysel Tıp Araştırma Enstitüsü Dergisi. 2018;8:23–32.
MLA Sürmen, Mustafa Gani vd. “Fosfoproteomik Uygulama Basamaklarına Genel Bakış”. Deneysel Tıp Araştırma Enstitüsü Dergisi, c. 8, sy. 1, 2018, ss. 23-32.
Vancouver Sürmen MG, Sürmen S, Pençe S. Fosfoproteomik Uygulama Basamaklarına Genel Bakış. Deneysel Tıp Araştırma Enstitüsü Dergisi. 2018;8(1):23-32.