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Shotgun identification of protein modifications from protein complexes and lens tissue

Academic Article
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Overview

authors

  • MacCoss, M. J.
  • McDonald, W. H.
  • Saraf, A.
  • Sadygov, R.
  • Clark, J. M.
  • Tasto, J. J.
  • Gould, K. L.
  • Wolters, D.
  • Washburn, M.
  • Weiss, A.
  • Clark, J. I.
  • Yates III, John

publication date

  • June 2002

journal

  • Proceedings of the National Academy of Sciences of the United States of America  Journal

abstract

  • Large-scale genomics has enabled proteomics by creating sequence infrastructures that can be used with mass spectrometry data to identify proteins. Although protein sequences can be deduced from nucleotide sequences, posttranslational modifications to proteins, in general, cannot. We describe a process for the analysis of posttranslational modifications that is simple, robust, general, and can be applied to complicated protein mixtures. A protein or protein mixture is digested by using three different enzymes: one that cleaves in a site-specific manner and two others that cleave nonspecifically. The mixture of peptides is separated by multidimensional liquid chromatography and analyzed by a tandem mass spectrometer. This approach has been applied to modification analyses of proteins in a simple protein mixture, Cdc2p protein complexes isolated through the use of an affinity tag, and lens tissue from a patient with congenital cataracts. Phosphorylation sites have been detected with known stoichiometry of as low as 10%. Eighteen sites of four different types of modification have been detected on three of the five proteins in a simple mixture, three of which were previously unreported. Three proteins from Cdc2p isolated complexes yielded eight sites containing three different types of modifications. In the lens tissue, 270 proteins were identified, and 11 different crystallins were found to contain a total of 73 sites of modification. Modifications identified in the crystallin proteins included Ser, Thr, and Tyr phosphorylation, Arg and Lys methylation, Lys acetylation, and Met, Tyr, and Trp oxidations. The method presented will be useful in discovering co- and posttranslational modifications of proteins.

subject areas

  • Acetylation
  • Amino Acid Sequence
  • CDC2 Protein Kinase
  • Cataract
  • Child, Preschool
  • Crystallins
  • Humans
  • Lens, Crystalline
  • Mass Spectrometry
  • Methylation
  • Molecular Sequence Data
  • Ovalbumin
  • Oxidation-Reduction
  • Phosphorylase a
  • Phosphorylation
  • Proteome
  • Schizosaccharomyces
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Identity

PubMed Central ID

  • PMC122992

International Standard Serial Number (ISSN)

  • 0027-8424

Digital Object Identifier (DOI)

  • 10.1073/pnas.122231399

PubMed ID

  • 12060738
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Additional Document Info

start page

  • 7900

end page

  • 7905

volume

  • 99

issue

  • 12

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