Mass Spectrometry Proteomics

Proteome analyses (i.e., the detection and characterization of the proteins being produced by a biological system at a given point in time) require high resolution protein separation to provide pure protein species for identification by mass analysis.  Liquid chromatography (high pressure liquid chromatography; HPLC) is currently the method of choice for high resolution separation of proteins and peptides without the size or charge bias inherent in electrophoresis separation procedures.  Mass analysis with the highest accuracy possible, as obtained by using tandem mass spectrometry (MS-MS) methods, is needed for accurate identification of proteins based on genome sequence database searches.

To provide flexibility in scientific research project planning, an instrument capable of determining the masses of both peptides and intact small proteins (i.e., 40, 000 D or smaller) is advantageous. The Argonne Biosciences Division proteome projects include those that require high-throughput sample analysis (e.g., protein expression quality assurance and protein modification analyses for the Midwest Center for Structural Genomics) as well as low-throughput with maximum information output analyses (i.e., complete protein inventory analyses for the Protein Mapping Group). The Argonne Biosciences Mass Spectrometry Core uses the ABI Q-Star XL quadrapole-TOF tandem mass spectrometer to provide the capability needed for this wide range of protein analyses. For current protein science research in the Biosciences Division, the Argonne Biosciences Mass Spectrometry Core utilizes state-of-the-art protein and peptide sample preparation methods together with nanoflow HPLC coupled to the tandem mass spectrometry capabilities for protein identifications based on tryptic peptide masses, as well as intact protein mass determinations for studies of protein modifications and ligand binding. New research initiatives are aimed toward using mass spectrometry based proteomics methods, together with metagenomics bioinformatics approaches, to identify proteins present in soil environments.