Quantitative analysis of complex protein mixtures using isotope-coded affinity tags

Gygi, Steven P., Rist, Beate, Gerber, Scott A., Turecek, Frantisek, Gelb, Michael H., Aebersold, Ruedi·1999·Nature Biotechnology
DOI 10.1038/13690

Cited by (1,009)

Items 101–200 of 1,009

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  3. Detection technologies in proteome analysis
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  4. Protein abundance profiling of the Escherichia coli cytosol
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  7. Streptavidin–biotin technology: improvements and innovations in chemical and biological applications
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  13. Mass spectrometric-based approaches in quantitative proteomics
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  15. Molecular profiling of human cancer
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    Parag Mallick, Bernhard Küster · 2010 · Nature Biotechnology
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    Deborah H. Lundgren, Sun‐Il Hwang, Linfeng Wu, David K. M. Han · 2010 · Expert Review of Proteomics
  22. Mapping Sites of O-GlcNAc Modification Using Affinity Tags for Serine and Threonine Post-translational Modifications
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    Hiroki Haraguchi · 2004 · Journal of Analytical Atomic Spectrometry
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    Boris Maček, Matthias Mann, Jesper Velgaard Olsen · 2008 · The Annual Review of Pharmacology and Toxicology
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    Huilin Zhou, Jeffrey A. Ranish, Julian D. Watts, Ruedi H. Aebersold · 2002 · Nature Biotechnology
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    Foss, Eric J, Radulovic, Dragan, Shaffer, Scott A, Ruderfer, Douglas M, Bedalov, Antonio, Goodlett, David R, Kruglyak, Leonid · 2007 · Nature Genetics
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    Bernhard Küster, Markus Schirle, Parag Mallick, Ruedi H. Aebersold · 2005 · Nature Reviews Molecular Cell Biology
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    Tom P. J. Dunkley, Rod B. Watson, Julian Leether Griffin · 2004 · Molecular & Cellular Proteomics
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    Veronika Vidová, Zdeněk Spáčil · 2017 · Analytica Chimica Acta
  57. Mass spectrometry
    John R. Yates, John R. Yates · 2000 · Trends in Genetics
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    Kunal Aggarwal · 2006 · Briefings in Functional Genomics and Proteomics
  60. Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries
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