Functional phosphoproteomic mass spectrometry-based approaches
1 Hospital Universitario Niño Jesús, Av. Menéndez Pelayo 65, 28009, Madrid, Spain
2 Clinical Sciences Lund, Skåne University Hospital and Lund University, Lund, SE-22185, Sweden
3 Hospital Universitario 12 de Octubre, Av. De Córdoba s/n, 28041, Madrid, Spain
4 Proteogenomics Research Institute for Systems Medicine, 11107 Roselle Street, San Diego, CA, 92121-1206, USA
Clinical and Translational Medicine 2012, 1:20 doi:10.1186/2001-1326-1-20Published: 5 September 2012
Mass Spectrometry (MS)-based phosphoproteomics tools are crucial for understanding the structure and dynamics of signaling networks. Approaches such as affinity purification followed by MS have also been used to elucidate relevant biological questions in health and disease.
The study of proteomes and phosphoproteomes as linked systems, rather than research studies of individual proteins, are necessary to understand the functions of phosphorylated and un-phosphorylated proteins under spatial and temporal conditions. Phosphoproteome studies also facilitate drug target protein identification which may be clinically useful in the near future.
Here, we provide an overview of general principles of signaling pathways versus phosphorylation. Likewise, we detail chemical phosphoproteomic tools, including pros and cons with examples where these methods have been applied. In addition, basic clues of electrospray ionization and collision induced dissociation fragmentation are detailed in a simple manner for successful phosphoproteomic clinical studies.