Seattle Proteome Center (SPC)
Proteomics Center at the Institute for Systems Biology

TECHNOLOGY MODULES

Technology Module A: Solid-phase stable isotope tag transfer chemistry

The objective of this module is to develop automatable and automated procedures for protein processing and stable isotope tagging. During the first period of funding, we will establish and validate experiments that will enable us to test different isotope tags and cleavable linkers, and start to systematically explore different chemistries. In years 2 and 3, the different chemistries will be optimized and commercialized.

Technology Module B: Selective isolation and stable isotope tagging of phosphorylated peptides

The objective of this module is to develop a new technology for the systematic and quantitative analysis of protein phosphorylation on a proteome-wide scale. During the first year of funding, we will establish and validate experiments that will enable us to selectively isolate and isotope tag phosphorylated peptides from complex mixtures. Initially, phosphopeptides containing SH groups will be tested building on the protocols developed in Technology Module A. In years 2 and 3, the analyses will be extended to use NH2-specific peptide trapping methods.

Technology Module C: Selective isolation and isotope tagging of peptides with lipid modifications

Technology Module D: Preparation of stable isotope tagged peptides for quantitative analysis of protein complexes

The objective of this module is to develop a new technology based on quantitative proteomics for the systematic and conclusive analysis of protein complexes, their components, stoichiometry, and dynamics of composition. During the first period of funding, we will establish basic protocols for the quantitative analysis of the components of protein complexes. In the first year, we will demonstrate that we can distinguish between specific and contaminating components of the complexes and that we can detect changes in abundance of complex components. The protocols will be transferred to the high throughput facility (HTPF) and applied to biology working group projects. In years 2 and 3, procedures to determine absolute quantification of complex components and, therefore, the stoichiometry of complexes will be developed and implemented.