Proteomics - Collaboration and Release Policy
Proteomic strategies: The primary goals of the proteomics component of the Discovery Initiative are to develop mass spectrometry and other proteomic methods for the identification of new migration related proteins, identify binding partners and identify utilized phosphorylation sites. Once methods are developed pilot analyses will be performed on a small number of major migration-related proteins. Another goal is to determine the changes in binding partners and utilized phosphorylation sites in response to growth stimuli and adhesion in a select subset of the initial targets. These analyses are challenging and time consuming and require collaborations among small groups of investigators, the Development Team. Consequently, progress is measured and not "high throughput".
Phosphoproteomics - While the goal is for 100% coverage of potential phosphorylation sites, under conditions of phosphatase inhibition and serum stimulation to maximize utilization o f sites, this cannot always be obtained. Therefore, determinations of utilized phosphorylation sites will be posted on this website within 6 weeks after 80% coverage has been achieved and validated, i.e., multiple repeats of a successful determination. The goal is to generate short, citable publications describing the sites and their significance. The graduate student or postdoc working on the project is allowed to withhold the posting of one phosphorylation site (from the determination of utilized sites) for up to 3 months following validation, at which time it will appear on the website with an asterisk and a note that it is under study. These are the only phoshorylation sites that can be studied by the Consortium or its collaborators prior to public release. Upon public release, the posted sites can be studied by anyone, however, we ask that you please acknowledge the CMC as the source of the site in any publications.
Binding partners - The goal is to determine the repertoire of proteins that associate with specific migration-related target proteins or co-purified with migration related organelles under a set of defined conditions. The analysis of immune complexes or purified organelles can yield a large number of associated proteins, whose interactions may or may not represent physiologic associations in the cell. It is also possible that some weakly associated proteins will not be detected. Therefore, these posted lists of putative associations should only be considered a starting point for further analysis. The results of the analyses will be posted on this website within 3 months of their validation, i.e., at least 3 repeats of a successful determination. The goal is to generate short, citable publications describing the sites and their significance. The Consortium laboratory working on a determination is allowed to withhold the posting of one putative binding protein for up to 3 months following validation. After 3 months, it will be posted on the website with an asterisk and a note that it is under study. These are the only binding partners that can be studied prior to public release. Upon public release, the putative binding partners can be studied by anyone, however, we ask that you please acknowledge the CMC as the source of the site in any publications.
While we may initiate collaborations for some of these determinations, the emphasis is on technology development, and therefore we do not have the capacity for high throughput analyses. However, we will make our protocols and procedures available on this website to facilitate the implementation of similar analyses at other sites. Please feel free contact us about our methods. If you are considering determinations that are similar to ours on migration related proteins, please contact us so that we can coordinate to avoid overlap or duplication of effort. In addition, if you wish us to assist in publicizing your determination or methodologies to the scientific community, we will list the results or protocols on our website.