National Resource for Mass Spectrometric Analysis of Biological Macromolecules

National Resource for Mass Spectrometric Analysis of Biological Macromolecules

Research Emphasis

The resource develops new mass spectrometric tools for studying biological processes involving proteins: the basic research focuses on investigations of techniques for volatilizing and ionizing proteins. It also designs and constructs mass spectrometric-based method to assist in the solution of challenging biological problems. The resource applies these tools to the solution of biological problems that involve, for example, the rapid identification of proteins, the elucidation of posttranslational modifications, and the definition of sites of functional interaction between biomolecules.

Current Research

Investigations of the matrix-assisted laser desorption ionization (MALDI) and electrospray ionization processes and the gas-phase fragmentation of biopolymers. Improved instrumentation for rapid, sensitive fragmentation analysis of peptides for protein identification. Improved instrumentation for ultra high-sensitivity detection of phosphopeptides. The origin of the "chemical noise" background and means for reducing it or its effects. Improved methodologies for studying protein interactions: ultimate goals include detecting single molecules of interest and making a map of all protein interactions within a cell, both stable and transient. Improved methods for studying protein phosphorylation: ultimate goal is to define the "phosphoproteome" of an organism. Development of a tool set for differential proteomics research that includes methods to accurately quantify changes in the levels of proteins and protein modifications. Development of mass spectrometry (MS) as a tool for the atomic resolution structure analysis of proteins, including integral membrane proteins and ion channels. Development of mass spectrometric informatics tools for analysis of the proteome and tools for annotating the human genome using mass spectrometric information.

Resource Capabilities

Instruments

In-house constructed ultraviolet-MALDI delayed extraction linear time-of-flight mass spectrometer; PerSeptive Biosystems STR MALDI-delayed extraction reflection time-of-flight mass spectrometer; Thermo-Finnigan LCQ electrospray ionization ion trap mass spectrometer for liquid chromatography MS (LCMS) and LCMS-MS of peptides; two in-house-constructed MALDI-ion trap mass spectrometers that use Thermo-Finnigan LCQ instruments; prototype Sciex Centaur Qq time-of-flight tandem mass spectrometer modified in-house with a MALDI ion source sensitive MS and MS/MS of peptides.

Software

Publicly accessible MS computer program/database is available at the Web site, along with a set of useful software tools (e.g., for protein identification spectrum manipulation and disulfide-mapping) that can access current information concerning any given protein or DNA sequence.

Special Features

This combination of instruments allows rapid identification of proteins, elucidation of posttranslational modification, determination of compactly folded protein domains, and determination of interactions between proteins.