News Updates Blog
April 2008
National Cancer Institute Mouse Proteomic Technologies Initiative Data Sets Released to Public on Tranche
The innovative scientific file sharing network and data repository, Tranche, has been chosen to host all Mouse Models proteomics data collected by the National Cancer Institute (NCI) Mouse Proteomic Technologies Initiative (MPTI) for public release.
In collaboration with Dr. Philip Andrews, University of Michigan, Department of Biological Chemistry and the Tranche team, the NCI MPTI project consortia deposited their mass spectrometry data sets into the Tranche data repository for storage and secure data sharing among participating research labs. See details about the MPTI projects below.
The data sets consist of analyses of tissue and serum from mouse models of multiple human cancers. The data sets are collected using a variety of analytical techniques and mass spectrometers, including LCQ, LTQ, and LTQ-FTICR instruments. The data sets are also available in publicly accessible formats such as mzXML and CPAS XAR files. Several laboratories, from both the MPTI Eastern Consortium and Western Consortium, participated in the project and produced large mass spectrometry data sets. These data sets have now been released for further studies by researchers around the world (http://mousemodels.tranche.proteomecommons.org).
Mouse proteomic data were uploaded to the distributed Tranche network, allowing the MPTI laboratories to securely share their data sets with collaborators. State-of-the-art data encryption methods are used by Tranche to ensure that data from individual labs remain private until the appropriate time for public release.
Given the unusually large quantity of data generated by mass spectrometry, Tranche is particularly well suited for its storage and dissemination. Currently Tranche hosts close to 1 terabyte of MPTI raw data and represents the largest single set of publicly raw proteomics data available on the network.
The Tranche network will continue to serve as an integral part of the data storage and dissemination for this project and other major proteomics projects. From the initial data collection and studies – and currently as a public repository – the high level of security, reliability and available storage space on the distributed Tranche network provides a convenient solution for these large data sets. Interested individuals, research groups and scholars can easily and freely access these data sets for further study
For more information on downloading these and other data sets, please visit: http://tranche.proteomecommons.org
For the Mouse Models data sets hosted by Tranche, please visit: http://mousemodels.tranche.proteomecommons.org
For more information about the NCI MPTI project, please visit: http://proteomics.cancer.gov/programs/mouse/consortia.asp
For more details regarding the Mouse Models project, contact Dr. Gil Omenn (University of Michigan) or Dr. Samir Hanash (Fred Hutchison Cancer Center) for the Eastern Consortium and Dr. Amanda Paulovich (Fred Hutchison Cancer Center) for the Western Consortium.
About Tranche:
The Tranche Project is an innovative free and open source file sharing tool that enables collections of computers to securely and easily share scientific data sets. Designed and built with scientists and researchers in mind, it provides a proper citation for the data sets, accommodates all licensing schemes, allows public or secure data sharing, provides for data persistence and assures that the data pedigree is known. Tranche has a novel structure that allows fully secure, traceable file transfer on a distributed network. It provides the strengths of a centralized file system with the benefits of a peer-to-peer network.
Scientific data sets are necessary for validating published work, designing software algorithms, aiding current and future research and represent a public resource of real value. However, sharing large amounts of scientific data is not currently an easy task. Data sets are frequently too large to share via e-mail or on a web server. A data set may contain hundreds of thousands of individual files or have an obscure format that makes it difficult to incorporate into centralized databases. File Transfer Protocol (FTP) sites have limitations and frequently disappear from the Internet because long-term support for the site often disappears when an individual leaves a research group or a server crashes after the funding period is over. Scientific data can also be hard to find, and frequently data can’t be shared because some level of confidentiality or restricted access must be guaranteed. The Tranche tool solves these issues and removes the obstacles commonly encountered in scientific data sharing.
For more information, visit: http://tranche.proteomecommons.org
Contacts:
Philip C. Andrews, Professor, NRPP Director
andrewsp@umich.edu
Mark Gjukich, Tranche Administrator
markgj@umich.edu
Department of Biological Chemistry
University of Michigan
300 N. Ingalls Street, Room 1123
Ann Arbor, MI 48109-0404
March 2008
To help move extremely large data sets onto the network, the Tranche Project is now offering free hard drive mail service. This enables a quick data upload and is easy for any researcher to get massive data sets uploaded with minimal effort. Best of all, we offer this as a free service!
If you would like to participate in this free service, please contact Mark Gjukich for more details or to get a drive sent out to your location
The Tranche network has recently exceeded 2 teraybytes of data uploaded. A significant milestone towards the goal of creating and maintaining a widely used data repository that isbecoming an integral part of scientific data sharing.
February
OxICAT approach to monitoring thiol redox developed with Jakob laboratory using mass spectrometry and ICAT stable isotope tag. Press Release
Reference:
Leichert LI, Gehrke F, Gudiseva HV, Blackwell T, Ilbert M, Walker AK, Strahler JR, Andrews PC, Jakob U. Quantifying changes in the thiol redox proteome upon oxidative stress in vivo. Proc Natl Acad Sci U S A. 2008 Feb 14; [Epub ahead of print].
Revisions made to the Tranche website. A major revamp of the the layout and user experience. New Quickstart Guides were posted to the site along with several other enhancements.