Research Article

Intregrated analysis of the human cardiac transcriptome, proteome and phosphoproteome

  1. Cristian I. Ruse1,2,
  2. Fen-Lai Tan2,
  3. Michael Kinter1,3,4,
  4. Meredith Bond1,2,*

Article first published online: 30 MAR 2004

DOI: 10.1002/pmic.200300682

Issue

PROTEOMICS

PROTEOMICS

Special Issue: PROTEOMIC FORUM 2003 Proceedings of the International Meeting on Proteome Analysis, Munich, Germany 14-17 September 2003

Volume 4, Issue 5, pages 1505–1516, May 2004

Additional Information

How to Cite

Ruse, C. I., Tan, F.-L., Kinter, M. and Bond, M. (2004), Intregrated analysis of the human cardiac transcriptome, proteome and phosphoproteome. Proteomics, 4: 1505–1516. doi: 10.1002/pmic.200300682

Author Information

  1. 1

    Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, OH, USA

  2. 2

    Department of Molecular Cardiology

  3. 3

    Department of Cell Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA

  4. 4

    Department of Chemistry, Cleveland State University, Cleveland, OH, USA

*Department of Physiology, University of Maryland School of Medicine, 655 West Baltimore Street, Baltimore, Maryland 21201, USA Fax: +1-410-706-8341

Publication History

  1. Issue published online: 21 APR 2004
  2. Article first published online: 30 MAR 2004
  3. Manuscript Received: 1 AUG 2003

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Keywords:

  • Database;
  • Mass spectrometry;
  • Protein phosphorylation;
  • Proteome;
  • Transcriptome

Abstract

Altered expression of different classes of genes has been shown to differentiate between failing and nonfailing human hearts. However, characterization of proteins and the post-translational modifications that regulate their functions is required for understanding both the physiology of cardiac muscle and the mechanisms leading to pathological states associated with cardiac diseases. We present in this paper, an analysis of the human cardiac transcriptome, proteome and phosphoproteome. Data from two sources (i) experiments performed in our laboratory and (ii) bioinformatics searches of public databases (SWISS-PROT, NCBI, Cardiac Gene Expression Knowledge Base, Gene Ontology Consortium and Affymetrix) are reported in a relational database that allows user-designed specific queries. Microarray experiments were performed with Affymetrix Hu95Av2. Cardiac proteins were digested with trypsin. An 11 step cation exchange procedure produced fractions for analysis in separate reversed phase high-performance liquid chromatography-tandem mass spectrometry (MS/MS) experiments. Immobilized metal affinity chromatography was used to select the phosphopeptides from the same tryptic peptide mixture. They were then further investigated by MS/MS. Gel-free approaches were used to detect 267 proteins and 47 phosphopeptides. Our human cardiac database contains 447 entries. We propose the use of this platform, built with data derived from nonfailing hearts, as a template for initiating the effort to characterize the human cardiac proteome and its associated post-translational modifications.

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