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

Erol E. Gulcicek1, Christopher M. Colangelo1, Walter McMurray1, Kathryn Stone1, Kenneth Williams1, Terence Wu1, Hongyu Zhao1, Heidi Spratt2, Alexander Kurosky2, Baolin Wu3

1 Yale University, New Haven, Connecticut, 2 University of Texas Medical Branch, Galveston, Texas, 3 University of Minnesota, Minneapolis, Minnesota
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 13.1
DOI:  10.1002/0471250953.bi1301s10
Online Posting Date:  July, 2005
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Abstract

In recent years, several proteomic methodologies have been developed that now make it possible to identify, characterize, and comparatively quantify the relative level of expression of hundreds of proteins that are coexpressed in a given cell type or tissue, or that are found in biological fluids such as serum. These advances have resulted from the integration of diverse scientific disciplines including molecular and cellular biology, protein/peptide chemistry, bioinformatics, analytical and bioanalytical chemistry, and the use of instrumental and software tools such as multidimensional electrophoretic and chromatographic separations and mass spectrometry. In this unit, some of the common protein‐profiling technologies are reviewed, along with the accompanying data‐analysis tools.

Keywords: Proteomics; Protein profiling; protein analysis; protein identification; serum biomarkers; computational tools; database searches

     
 
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Table of Contents

  • Gel‐Based Approaches
  • Non‐Gel Based Approaches
  • SELDI/MALDI‐MS‐Based Disease Biomarkers
  • Protein Microarrays
  • Analysis of Protein Profiling Data
  • Gel‐Based Data Analysis
  • MS‐Based Protein Profiling Software Analysis
  • Disease Biomarker Analysis
  • Conclusions
  • Acknowledgements
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Literature Cited

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Internet Resources
   http://www1.qiagen.com/literature/handbooks/PDF/Protein/Purification/QXP_Phospho‐Protein/1023373HB_QXP_Phos_122002WW.pdf
  Information on Qiagen commercial phosphoprotein affinity kits
   http://www.proteomesystems.com
  Web sites for companies selling liquid‐based isoelectric focusing fractionation apparatus
   http://www.invitrogen.com
  Institute for Systems Biology Web site specifically for proteomics project analysis and management
   http://db.systemsbiology.org/projects/sbeams/
  A Global Proteome Machine (GPM) Organization Web site for proteomics project analysis and management
   http://www.thegpm.org/
  Yale Protein Expression Database (YPED), a Yale University Web site for proteomics project analysis, management, and archiving (in development)
   http://info.med.yale.edu/proteome/
  Site for downloading a machine‐learned intensity‐based protein identification software application called SILVER
   http://llama.med.harvard.edu/Software.html
  Institute for Systems Biology Web site showcasing all of their Proteomics analysis tools
   http://www.proteomecenter.org/software.php
  BD Biosciences Clontech company Web site for protein antibody microarray products
   http://www.bdbiosciences.com/clontech/archive/JUL04UPD/antibody_microarray.shtml
  Web site forProtometrix, which developsg and sells protein microarrays (now part of Invitrogen)
   http://www.protometrix.com/
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