Biological MS Data and Software Distribution Center
The mass spectrometry capabilities at Pacific Northwest National Laboratory (PNNL) are primarily applied to biological research, with an emphasis on proteomics and metabolomics. Many of these cutting-edge mass spectrometry capabilities and bioinformatics methods are housed in the Department of Energy's Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility operated by PNNL. These capabilities have been developed and acquired through cooperation between the EMSL national scientific user program and PNNL programmatic research.
In addition to the state-of-the-art capabilities, the mass spectrometry laboratories are equipped with methodologies to perform sample preparation and storage, chemical synthesis and derivatization, instrument development and experimentation, genetics studies, free-flow electrophoresis, and more. Extensive resources are also available for biochemical and molecular biology manipulations.
The Mass Spectrometry Special Interest Group (MS-SIG) is holding a symposium in Berlin Germany featuring prominent researchers in the field of proteomics, including Jurgen Cox, Oliver Kohlbacher, Olga Vitek, and others. This one day symposium, which occurs just prior to the ISMB/ECCB 2013 conference, will have two sessions on:
- Protein identification/modification/quantification
- Data integration & Proteomics applications in biology and medicine
The purpose of this site is to provide access to information pertaining to many of the projects related to mass spectrometry and separations performed at PNNL/EMSL. You will find the following resources available through this site:
- PNNL-developed software tools and source code
- PNNL-generated raw data and processed results from our research
- Descriptions of PNNL's research and how you can collaborate
- Information to help you access and use the available data and software
- Links to publications that used the data and results available on this site
- Tutorials and user manuals
For more information about this national user facility and how to submit proposals for access to these and other resources, please visit EMSL: Environmental Molecular Sciences Laborabory
If you would like to learn more about some of the major programs represented that generated the data and software available on this site, in addition to contact information regarding collaborative opportunities, please see:
- PNNL's Resarch Center for Integrative Biology (BTRC)
- Biological and Environmental Research at PNNL
- Systems Biology at PNNL
- Center for Systems Biology of EnteroPathogens
Using the Site
Experimental metadata and applications software can be freely accessed and/or downloaded without creating an account and without logging into the system. In order to be able to download actual experimental data (instrument data files and analysis results), you will need to register for a free account. A temporary password will then be emailed to an address you provide. You may then access the system to change your password to one of your choosing, then login to download data.
All of the data and software packages on the site are available free of charge.
All publications that result from the use of information from this center should include the following acknowledgment statement:
Results are from experimental data that were obtained by the Proteomics group at Pacific Northwest National Laboratory (PNNL)
in Richland, Washington. Portions of this research were supported by the NIH National Center for Research Resources (RR18522),
and the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the
U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL).
PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.
Contact Dr. R.D. Smith, Director of Proteomics Research, with questions.