Challenges and solutions in proteomics

Hongzhan Huang, Hem D. Shukla, Cathy Wu, Satya Saxena

Research output: Contribution to journalReview article

Abstract

The accelerated growth of proteomics data presents both opportunities and challenges. Large-scale proteomic profiling of biological samples such as cells, organelles or biological fluids has led to discovery of numerous key and novel proteins involved in many biological/disease processes including cancers, as well as to the identification of novel disease biomarkers and potential therapeutic targets. While proteomic data analysis has been greatly assisted by the many bioinformatics tools developed in recent years, a careful analysis of the major steps and flow of data in a typical high-throughput analysis reveals a few gaps that still need to be filled to fully realize the value of the data. To facilitate functional and pathway discovery for large-scale proteomic data, we have developed an integrated proteomic expression analysis system, iProXpress, which facilitates protein identification using a comprehensive sequence library and functional interpretation using integrated data. With its modular design, iProXpress complements and can be integrated with other software in a proteomic data analysis pipeline. This novel approach to complex biological questions involves the interrogation of multiple data sources, thereby facilitating hypothesis generation and knowledge discovery from the genomic-scale studies and fostering disease diagnosis and drug development.

Original languageEnglish (US)
Pages (from-to)21-28
Number of pages8
JournalCurrent Genomics
Volume8
Issue number1
DOIs
StatePublished - Mar 2007

Keywords

  • Bioinformatic tools
  • Biomarkers
  • High-throughput analysis
  • Pathway discovery
  • Proteomic profiling
  • Sequence library
  • Stage specific proteins
  • iProXpress

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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    Huang, H., Shukla, H. D., Wu, C., & Saxena, S. (2007). Challenges and solutions in proteomics. Current Genomics, 8(1), 21-28. https://doi.org/10.2174/138920207780076910