Proteomics and the Analysis of Proteomic Data: 2013 Overview of Current Protein‐Profiling Technologies

Can Bruce1, Kathryn Stone1, Erol Gulcicek1, Kenneth Williams1

1 W.M. Keck Foundation Biotechnology Resource Laboratory and Molecular Biochemistry and Biophysics Department, Yale University, New Haven, Connecticut
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 13.21
DOI:  10.1002/0471250953.bi1321s41
Online Posting Date:  March, 2013
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Mass spectrometry has become a major tool in the study of proteomes. The analysis of proteolytic peptides and their fragment ions by this technique enables the identification and quantitation of the precursor proteins in a mixture. However, deducing chemical structures and then protein sequences from mass‐to‐charge ratios is a challenging computational task. Software tools incorporating powerful algorithms and statistical methods improved our ability to process the large quantities of proteomics data. Repositories of spectral data make both data analysis and experimental design more efficient. New approaches in quantitative and statistical proteomics make possible a greater coverage of the proteome, the identification of more post‐translational modifications, and a greater sensitivity in the quantitation of targeted proteins. Curr. Protoc. Bioinform. 41:13.21.1‐13.21.17. © 2013 by John Wiley & Sons, Inc.

Keywords: shotgun proteomics; search engines; labeled quantitation; data repository; Selective Reaction Monitoring; data‐independent analysis; data exchange format; quantitative proteomics

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Table of Contents

  • Introduction
  • Discovery Proteomics
  • Quantitative Proteomics
  • Conclusion
  • Acknowledgments
  • Literature Cited
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Literature Cited

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