Protocol

Mass Spectrometry Data Analysis in Proteomics

Volume 1007 of the series Methods in Molecular Biology pp 359-377

Date:

Proteomic Strategies to Characterize Signaling Pathways

  • H. C. HarshaAffiliated withInstitute of Bioinformatics, International Technology Park
  • , Sneha M. PintoAffiliated withInstitute of Bioinformatics, International Technology Park
  • , Akhilesh PandeyAffiliated withDepartments of Biological Chemistry, Pathology, and Oncology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University

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Abstract

Cells respond to external stimuli by transducing signals through a series of intracellular molecules and eliciting an appropriate response. The cascade of events through which the signals are transduced include post-translational modifications such as phosphorylation and ubiquitylation in addition to formation of multi-protein complexes. Improvements in biological mass spectrometry and protein/peptide microarray technology have tremendously improved our ability to probe proteins, protein complexes, and signaling pathways in a high-throughput fashion. Today, a single mass spectrometry-based investigation of a signaling pathway has the potential to uncover the large majority of known signaling intermediates painstakingly characterized over decades in addition to discovering a number of novel ones. Here, we discuss various proteomic strategies to characterize signaling pathways and provide protocols for phosphoproteomic analysis.

Key words

Signaling pathways Mass spectrometry Phosphorylation Enrichment of phosphoproteomes Quantitative phosphoproteomics Cancer