The Collaboratory for MS3D (C-MS3D) is a knowledge grid for the biology community with data/metadata management, security, application integration, collaboration tools, analysis capabilities, and research tools. This work is being carried out in direct collaboration with scientists leading the development of MS3D, a new method that combines intramolecular chemical crosslinking with high-resolution mass spectrometry to glean structural information about proteins and other biological macromolecules.

This collaboratory is built on infrastructure technologies developed by the DOE-funded Scientific Annotation Middleware (SAM) and the Collaboratory for Multi-scale Chemical Sciences (CMCS) projects.

As part of the Collaboratory for MS3D, several MS3D tools have been developed or refined and made available to the public through the portal:

• Links: A program to analyze mass spectrometric data generated from native, modified, and crosslinked protein and nucleic acid digests.
   
• MS2Links: A program used for assigning tandem MS peak lists generated from the fragmentation of crosslinked, modified or unmodified peptides, proteins and/or nucleic acids.
   
• XLBase: An annotated crosslinkers database which supports experimental design and interpretation of crosslinking data.
   
• MS3D Workflow: A workflow tool that assists users with the various stages of a typical MS3D workflow.

To go to the C-MS3D Portal, click on "The C-MS3D Portal" at the top or at the bottom of the page.