The Collaboratory for MS3D: A New Cyberinfrastructure for the Structural Elucidation of Biological Macromolecules and Their Assemblies Using Mass Spectrometry-Based Approaches

Abstract

Modern biomedical research is evolving with the rapid growth of diverse data types, biophysical characterization methods, computational tools and extensive collaboration among researchers spanning various communities and having complementary backgrounds and expertise. Collaborating researchers are increasingly dependent on shared data and tools made available by other investigators with common interests, thus forming communities that transcend the traditional boundaries of the single research lab or institution. Barriers, however, remain to the formation of these virtual communities, usually due to the steep learning curve associated with becoming familiar with new tools, or with the difficulties associated with transferring data between tools. Recognizing the need for shared reference data and analysis tools, we are developing an integrated knowledge environment that supports productive interactions among researchers. Here we report on our current collaborative environment, which focuses on bringing together structural biologists working in the area of mass spectrometric based methods for the analysis of tertiary and quaternary macromolecular structures (MS3D) called the Collaboratory for MS3D (C-MS3D). C-MS3D is a web-portal designed to provide collaborators with a shared work environment that integrates data storage and management with data analysis tools. Files are stored and archived along with pertinent meta data in such a way as to allow file handling to be tracked (data provenance) and data files to be searched using keywords and modification dates. While at this time the portal is designed around a specific application, the shared work environment is a general approach to building collaborative work groups. The goal of which is to not only provide a common data sharing and archiving system but also to assist in the building of new collaborations and to spur the development of new tools and technologies.

Enhanced In-Source Fragmentation in MALDI-TOF-MS of Oligonucleotides Using 1,5-Diaminonapthalene

“…Typically, from 250 to 1000 individual laser shots were averaged for each MS or MS/MS spectrum. Assignment of observed fragment ions was performed using Web-accessible DNA/RNA MS bioinformatics software: Mongo Oligo Calculator (http://library.med.utah.edu/masspec/mongo.htm) and MS2Links [27]. (Additional methodological considerations may be found in the online supplementary materials.…”

Structural Basis of G Protein-coupled Receptor-Gi Protein Interaction

“…Data analyses were performed with the aid of on-line server MS3D (24,25). First, the precursor peptide ions from LC-MS/MS were screened by the "Links" program from MS3D.…”

“…The peptide mixtures resulting from in-gel digestions were analyzed by LC-MS/MS mass spectrometry. Data analysis was performed with the aid of the on-line server MS3D (24). The MS/MS spectrum of each candidate peptide was then manually checked to see whether it is a validated CB 2 -G protein cross-linked peptide.…”

<formula formulatype="inline"><tex Notation="TeX">${\rm MS2DB}+$</tex></formula>: A Software for Determination of Disulfide Bonds Using Multi-Ion Analysis

“…In Table II, we present different metrics describing the performance of the method on a set of ten proteins having varying disulfide bond topologies. Comparative analysis conducted in [5] indicate that results from were comparable or better than those obtained with the two gold standards in the area, MassMatrix [2] and MS2Links [3].…”