Antibody-based Protein Profiling of the Human Chromosome 21

Mol Cell Proteomics. 2012 Mar;11(3):M111.013458. doi: 10.1074/mcp.M111.013458. Epub 2011 Oct 31.

Abstract

The Human Proteome Project has been proposed to create a knowledge-based resource based on a systematical mapping of all human proteins, chromosome by chromosome, in a gene-centric manner. With this background, we here describe the systematic analysis of chromosome 21 using an antibody-based approach for protein profiling using both confocal microscopy and immunohistochemistry, complemented with transcript profiling using next generation sequencing data. We also describe a new approach for protein isoform analysis using a combination of antibody-based probing and isoelectric focusing. The analysis has identified several genes on chromosome 21 with no previous evidence on the protein level, and the isoform analysis indicates that a large fraction of human proteins have multiple isoforms. A chromosome-wide matrix is presented with status for all chromosome 21 genes regarding subcellular localization, tissue distribution, and molecular characterization of the corresponding proteins. The path to generate a chromosome-specific resource, including integrated data from complementary assay platforms, such as mass spectrometry and gene tagging analysis, is discussed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Antibodies, Monoclonal / immunology*
  • Blotting, Western
  • Cells, Cultured
  • Chromatography, Liquid
  • Chromosomes, Human, Pair 21 / genetics*
  • Chromosomes, Human, Pair 21 / metabolism*
  • Databases, Factual
  • Fluorescent Antibody Technique
  • Gene Expression Profiling*
  • Humans
  • Immunoenzyme Techniques
  • Isoelectric Focusing
  • Kidney / cytology
  • Kidney / metabolism
  • Mass Spectrometry
  • Molecular Sequence Data
  • Peptide Fragments / metabolism
  • Proteome / analysis*
  • Proteome / immunology*
  • Proteomics*
  • Sequence Analysis, RNA
  • Sequence Homology, Amino Acid
  • Software
  • Subcellular Fractions

Substances

  • Antibodies, Monoclonal
  • Peptide Fragments
  • Proteome