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National Cancer Institute Mouse Proteomics Technologies Initiative Data Hosted by Tranche from Eastern and Western Consortia

Jump to publicly released data sets.

The National Cancer Institute (NCI) Mouse Proteomics Technologies Initiative (MPTI) project deposited its datasets in Tranche for public access. Given the unusually large quantity of data generated (close to a terabyte) the data set is particularly well suited for storage in Tranche. This page documents the exact data sets published and attempts to provide a public record of as much information related to the data set as possible, e.g. mouse models used, contact info, mass spectrometers, etc. Do note that for any of the data sets you can use Tranche to download any portion of the overall data -- you need not download all data sets. With this collaboration we hope that the NCI and Tranche team have elevated the standard by which raw proteomics data and information is collected and of true public availability.

If you are citing the NCI MPTI data set in Tranche, please use this citation information:

• Link to this page: http://tranche.proteomecommons.org/examples/nci-mouse-models/
• Citation for Tranche: http://tranche.proteomecommons.org

Please note that the scope of the NCI MPTI and Tranche collaboration is limited to simply providing a public archive of the MPTI data set. Not to necessarily provide tools for reprocessing and analyzing the data. The CPAS project was funded for this purpose and several publications have been released describing the data -- Tranche was selected as a public archive after the MPTI study concluded.

The page is divided into the following sections. Please provide any comments, suggestions, or updates to the Tranche user's list.

• Information and download links for all MPTI data sets
• A quick method for downloading all raw data
• Help! The upload tool won't start on my computer.

Other helpful information

• Credits and References for this collaboration
• NCI Mouse Proteomic Technologies Initiative (MPTI) Homepage
• About the Initiative
• Role of the Mouse
• Consortia Members
• Mouse Models Chart
• Mouse Initiative Bibliography

Information and download links for Mouse Proteomics Technologies Initiative data sets

Many labs participated in the NCI's Mouse Proteomics Technologies Initiative project and many of those labs produced several data sets. Archiving these data into Tranche consisted of uploading data from each lab and encrypting each data set individually. The encryption was required in order to ensure that individual lab's data remained private until the appropriate time to publicly release it.

This data has officially been made public for download and research.

• Eastern Consortium Data
• Western Consortium Data
• Data Analysis of Eastern and Western Consortium Datasets

Eastern Consortium Mouse Proteomics Technologies Initiative Data Sets

Western Consortium Mouse Proteomics Technologies Initiative Data Sets

Much of the Western Consortium data is on-line; however, we are still working on populating several descriptive fields relating to the data sets.

* Published works based on data sets can be located here:
"Head-to-Head Comparison of Serum Fractionation Techniques," J. Proteome Res., 6 (2), 828 -836, 2007. 10.1021/pr0604920
"Integrated Pipeline for Mass Spectrometry-Based Discovery and Confirmation of Biomarkers Demonstrated in a Mouse Model of Breast Cancer," J. Proteome Res., 6 (10), 3962 -3975, 2007. 10.1021/pr070202v

Data Analysis of Eastern and Western Consortium Datasets

This tables links to known bioinformatics analysis of the NCI Mouse Proteomics Technologies Initiative data sets. If you have an analysis to add or know of a data set that is missing, please contact the Tranche Users e-mail list for help updating this page and uploading your data and or or analysis to Tranche.

Click the "More Info." next to each analysis for a synopsis of what data sets were used, publications related to the analysis, and other information related to the analysis.

A quick method for downloading all raw data

If you are interested in a quick method to download all of the NCI Mouse Proteomics Technologies Initiative data sets, please post to the Tranche Users discussion list. You should be able to accomplish this without having to download each data set individually.

Help! The upload tool won't start on my computer.

Generally the Java-based upload tool will work on most computers. We require that you have at least a version of Java installed that was released within the past four years. Most every current computer comes with this automatically. If for some reason you don't have Java installed, you can freely download and install the latest version from Sun Microsystem's website. Here is a tutorial.

Credits/References

Tranche work and design of this website.

• Jayson A. Falkner
• Philip C. Andrews, Ph.D.

Design, support, and collaboration from NCI MPTI

• Henry Rodriguez (NIH/NCI)
• Chris Kingsinger
• Adam Clark

NCI MPTI Consortia Members

The "Eastern Consortium" is based at the University of Michigan (Ann Arbor, MI), and includes:

• Dana Farber Cancer Institute (Boston, MA)
• Fred Hutchinson Cancer Research Center (Seattle, WA)
• Harvard-Partners Center for Genetics and Genomics (Cambridge, MA)
• Massachusetts Institute of Technology (Cambridge, MA)
• Memorial Sloan-Kettering Cancer Center (New York, NY)
• Van Andel Research Institute (Grand Rapids, MI)
• University of Michigan (Ann Arbor, MI)

Samir M. Hanash, M.D., Ph.D., Dept. of Pediatrics, is founding PI at the University of Michigan (10/04-11/06) followed by Gil Omenn, M.D., Ph.D., Internal Medicine, CCMB, University of Michigan (11/06-present).

The "Western Consortium" is based at the Fred Hutchinson Cancer Research Center (Seattle, WA), and includes:

• Institute for Systems Biology (Seattle, WA)
• Pacific Northwest National Laboratory (Richland, WA)
• Plasma Proteome Institute (Washington, DC)
• Fred Hutchinson Cancer Research Institute (Seattle, WA)

Martin W. McIntosh, Ph.D., and Amanda Paulovich, M.D., Ph.D., Computational Proteomics Laboratory, Fred Hutchinson Cancer Research Center, are the lead investigators of the Western Consortium.