The goal of the Proteomics Facility is to provide investigators with the capabilities to identify, characterize and quantify the proteins present in tissues, cells and biological fluids. Through the development of advanced methods, the Facility aims to assist members with solving difficult or previously intractable problems in biomedical research. Methods for protein and peptide isolation, separations, quantification, identification and bioinformatics analysis, together with expert guidance in study design, are integrated into expertise offered by the Facility. The Facility has access to several analytical technologies thereby allowing investigators to adopt multiple strategies and to independently verify their findings. The Facility also provides training in proteomics analysis and experimental design.

Several advancements have been made to the search engine Protein Prospector over the past 3 years. This suite of protein informatic tools is now able to batch search tandem mass spectrometry data files and perform protein quantification for a number of stable isotope methods. The new implementation of expectation values reduces the number of false positives while increasing the number of correct identifications. Two recent publications in MCP detail some of the recent developments.

The Association of Biomolecular Resouce Facilities (ABRF) sponsors yearly studies to assist proteomics research labs and cores evaluate their capabilities to identify and characterize "unknown" protein samples. The goal is to evaluate the technologies and educate their members. Results of past studies are posted on their site. These studies have aimed to address groups abilities to identify proteins in a simple mixture, identification of phosphorylation sites, discrimination of protein isoforms, and accuracy of de novo peptide sequencing.

The facility is a collaborative research resource that balances applied proteomics research with the development of new and improved methods for protein identification and quantification. The facility encourages collaborations that apply the tools of proteomics to biomedical research. Prospective users are encouraged to contact Dr. Kirk Hansen (303 724-3325) or Dr. Mark Duncan

The Proteomics Facility is housed within the Mass Spectrometry Research Center on the ground floor of RC-1 South at the Fitzsimons campus.

The facility participates in a series of short courses relating to aspects of mass spectrometry and proteomics. Both lecture-based and hands-on courses are available, and these are open to outside participants. If you are interested in attending any of these please email Melissa Ramirez.

Work performed in or by the Facility should be acknowledged. A reprint of all publications and presentations that include data obtained in the/by the facility are retained for our records. This assists us to document activities and aids us in gaining funding to maintain and upgrade the facility.

As part of the HUPO Human Antibody Initiative the Protein Atlas aims to show the expression and localization of proteins in a large variety of normal human tissues and cancer cells. The data is presented as high resolution images representing immunohistochemically stained tissue sections.