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Biomedical Technology Resources Directory

Mass Spectrometry

 
Bio-Organic Biomedical Mass Spectrometry Resource
Mass Spectrometry Resource for Biology and Medicine
National Resource for Biomedical Accelerator Mass Spectrometry
National Resource for Mass Spectrometric Analysis of Biological Macromolecules
Resource for Biomedical and Bio-organic Mass Spectrometry

 
Bio-organic Biomedical Mass Spectrometry Resource
University of California, San Francisco
521 Parnassus, Room 1124S
San Francisco, CA 94143-0446
http://donatello.ucsf.edu/

Grant No. P41 RR001614
Principal Investigator and Contact
A. L. Burlingame, Ph.D.
415-476-5641; Fax: 415-476-0688
E-mail: alb@itsa.ucsf.edu

Research Emphasis

The resource focuses on mass spectrometric techniques for sequencing and quantitation of peptides and structural characterization of modified proteins and glycoconjugates; microsample handling and mass spectrometric analysis at the femtomole to attomole level, such as in identification of proteins separated by 2-D gel electrophoresis using silver and fluorescence detection; cotranslational and posttranslational modifications of proteins, including glycosylation, phosphorylation, sulfation, acylation, etc.; and xenobiotic modification, such as that arising from mechanism-based enzyme inhibition and drug–protein adduct formation. Methodology includes matrix-assisted laser desorption ionization with high-energy collision-induced dissociation analysis and capillary HPLC-nanoflow rate electrospray tandem mass spectrometry.

Current Research

Molecular and cellular proteomics, drug metabolic activation, and protein adduct identification; studies of protein machines, complexes and signaling cascades, and structural biology; studies of Conus peptides that are blockers of ion channels and neurotransmission. In addition, development of multidimensional ion exchange and reverse phase separations of affinity separated, isotopically labeled peptides from cell culture and in vivo systems employing new acid cleavable, carbon-13 coded ICAT reagents. Development of complementary offline chromatographic (MALDI-CIDMS) and online (ESI-CIDMS) strategies for comprehensive detection and sequencing of ICAT-labeled systems. Development of electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) and tandem technologies for determination of biomolecular and structural studies of proteins, noncovalent and covalent protein assemblages, heterobiopolymers, and glycoconjugates.

Resource Capabilities

Instruments

PerSeptive Biosystems MALDI Voyager Elite and Voyager Elite STR DE reflectron time-of-flight (TOF) mass spectrometers, Mariner ES oaTOF mass spectrometers, Sciex API 300 ES triple quadrupole mass spectrometer, nanoflow rate electrospray quadrupole orthogonal acceleration TOF mass spectrometer (QqTOFMS)-PE Sciex PULSAR/Q STAR, automated ABI MALDI TOF TOFMS(ABI 4700 Proteomics Analyzer) with 24-plate cassette sample system and VG 70S mass spectrometer.

Special Features

MALDI high-energy CID capability for de novo protein sequence determination and structural analysis. Online capillary HPLC electrospray mass spectrometry and offline capillary HPLC matrix-assisted laser desorption tandem mass spectrometry for identification of 1-D and 2-D gel spots as well as solution protein mixtures from immunoprecipitates, fusion baits, and tandem affinity tags, etc. Bioinformatics tools such as MS-Fit, MS-Tag, and MS-Homology. Web-accessible algorithms for gene and EST database interrogation with mass spectral data via ProteinProspector.

  1. Liu, B., Huang, L., Sihlbom, C., Burlingame, A. L., and Marks, J. D., Towards proteome-wide production of monoclonal antibody by phage display. Journal of Molecular Biology 315:1063–1073, 2002.
  2. Greenbaum, D., Baruch, A., Hayrapetian, L., Darula, Z., Burlingame, A. L., et al., Chemical approaches for functionally probing the proteome. Molecular Cellular Proteomics 1:60–68, 2002.
  3. Allen, N.P.C., Patel, S. S., Huang, L., Chalkley, R. J., Burlingame, A. L., Lutzmann, M., Hurt, E. C., and Rexach, M., Deciphering networks of protein interactions at the nuclear pore complex. Molecular Cellular Proteomics 1:930–946, 2002.
  4. Zhang, K., Williams, K. E., Huang, L., Yau, P., Siino, J. S., Bradbury, E. M., Jones, P. R., Minch, M. J., and Burlingame, A. L. Histone acetylation and deacetylation: Identification of acetylation and methylation sites of HELA histone H4 by mass spectrometry. Molecular Cellular Proteomics 1:500–508, 2002.
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Mass Spectrometry Resource for Biology and Medicine
Boston University School of Medicine
Departments of Biochemistry and Biophysics
715 Albany Street, R-806
Boston, MA 02118-2526

www.bumc.bu.edu/msr

Grant No. P41 RR010888
Principal Investigator and Contact
Catherine E. Costello, Ph.D.
617-638-6490; Fax: 617-638-6491
E-mail: cecmsms@bu.edu

Coprincipal Investigator
Joseph Zaia, Ph.D.
617-638-6762; Fax: 617-638-6761
E-mail: jzaia@bu.edu

Research Emphasis

The resource’s mission is to conduct high-sensitivity structural determinations and analyses of biological compounds via mass spectrometry (MS). An emphasis is on glycoconjugates, oligosaccharides, and proteins; and structure-activity studies related to immunology, carcinogenesis, developmental biology, parasitology, and infectious diseases; biophysical properties of carbohydrates and glycoconjugates; carbohydrate and amino acid sequence determinations of glycoproteins and proteins; and structure elucidation of unusual residues and posttranslational modifications.

Current Research

Electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) methods for high-sensitivity structural determinations. Chromatographic and electrophoretic methods for analysis of complex mixtures. Derivatization and degradation protocols (low/sub pmol) with emphasis on maximizing the MS structural information. Ion chemistry studies to improve sensitivity and elucidate fragmentation patterns of native and derivatized biopolymers. MALDI methods for surface analysis. Fourier transform ion cyclotron resonance (FT-ICR) MS in biological studies. Atomic force microscopy (AFM) to complement MS studies.

Resource Capabilities

Instruments

ThermoQuest GC-Qplus GC/MS. VG/Fisons Quattro II triple quadrupole tandem MS with HPLC, Z-spray, and atmospheric pressure chemical ionization; may be operated in MS or MS/MS modes. Two Sciex/Applied Biosystems Q-Star quadrupole orthogonal acceleration TOF mass spectrometers with MALDI and ESI sources, capHPLC. Bruker Reflex IV and Finnigan MAT Vision 2000 MALDI reflectron TOF MS with nitrogen (UV, 337 nm) and Er:YAG (infrared, 2.94 mm) lasers operated in linear, reflectron, and post-source decay modes to yield MW information and structural details. Two IonSpec Ultima FT-ICR mass spectrometers with external MALDI and ESI sources, 7 T active-shielded magnets, MSn capabilities with selected ion decomposition by SORI-CID, infrared multiphoton dissociation and electron capture dissociation (ECD), high-resolution accurate mass measurements. AFM to be added in late 2002.

Special Features

Guidance on sample preparation and data interpretation. By special arrangement: Microscale derivatizations, chemical, and enzymatic degradations. FT-ICR MS research focuses on carbohydrate sequencing strategies, high-pressure MALDI, ECD, and software development for instrument control, and data interpretation.

  1. Lim, A., Prokaeva, T., McComb, M. E., O’Connor, P. B., Théberge, R., Connors, L. H., Skinner, M., and Costello, C. E., Characterization of transthyretin variants in familial transthyretin amyloidosis by mass spectrometric peptide mapping and DNA sequence analysis. Analytical Chemistry 74:741–751, 2002.
  2. McClellan, J. E., Costello, C. E., O’Connor, P. B., and Zaia, J., Influence of charge state on product ion mass spectra and the determination of 4S/6S sulfation sequence of chondroitin sulfate oligosaccharides. Analytical Chemistry 74:3760–3771, 2002.
  3. O’Connor, P. B., Mirgorodskaya, E., Costello, C. E., et al., High pressure matrix-assisted laser desorption/ionization Fourier transform mass spectrometry for minimization of ganglioside fragmentation. Journal of the American Society for Mass Spectrometry 13:402–407, 2002.
  4. Hopkins, C. E., O’Connor, P. B., Allen, K. N., Costello, C. E., and Tolan, D. R., Chemical-modification rescue assessed by mass spectrometry demonstrates g-thia-lysine yields the same activity as lysine in aldolase. Protein Science 11:1591–1599, 2002.
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National Resource for Biomedical Accelerator Mass Spectrometry
University of California
Lawrence Livermore National Laboratory
P.O. Box 808, L-452
7000 East Avenue
Livermore, CA 94551-0808
www.llnl.gov/bioams/

Grant No. P41 RR013461
Principal Investigator
Kenneth W. Turteltaub, Ph.D.
925-423-8152; Fax: 925-422-2282
E-mail: turteltaub2@llnl.gov

Contact
Karolyn Burkhart-Schultz
Resource Manager
925-422-6796; Fax: 925-422-8657
E-mail: burkhartschultz1@llnl.gov

Research Emphasis

The National Resource for Biomedical Accelerator Mass Spectrometry (AMS) was established to make AMS available to biomedical researchers who have a need for accurately measuring very low levels of 14C while conducting their research. The resource has three major functions: To develop new methods and instrumentation for the use of AMS in biomedical research; to provide biological researchers with access to AMS through collaboration or service arrangements; and to provide outreach activities to educate researchers and students on AMS.

Current Research

The focus of this resource is the development of new instrumentation and methods for the use of AMS in biomedical research and demonstration of new applications. The present emphasis is the development of automated methods for sample preparation, demonstration of smaller spectrometers, investigation of methods to study protein biochemistry and cell biology, and development of isotope derivatization approaches. The aim is to provide analysis of 14C and/or 3H in tissues, macromolecules, and metabolite extracts. Applications under investigation include the effects of toxicants in humans; identification of protein targets for drugs, nutrients, and toxicants; determination of the pharmacokinetics of micronutrients; and understanding the role of genotype in disease mechanisms.

Resource Capabilities

Lawrence Livermore National Laboratory is a national laboratory organized to facilitate multidisciplinary sharing of facilities. The AMS resource supports biomedical laboratories and a wide range of equipment for the characterization and analysis of biological samples. It supports sample preparation laboratories for the conversion of biological samples containing 14C and 3H to forms capable of being analyzed efficiently by AMS.

Instruments

A 1-megaVolt spectrometer dedicated to biochemical quantitation forms the core instrumentation, with access to a 10-MV spectrometer possible on a time-available basis. The spectrometers consist of a cesium sputter source, low-energy injection beamline, a high-energy mass spectrometer, and an ionization detector for energy measurements. Approximately 100 samples containing 1 attomole to 1 picomole of 14C are measured per 8 hours on either spectrometer.

  1. Lu, C. M., Burton, D. W., Fitzgerald, R. L., et al., Mass spectrometric immunoassay for parathyroid related protein. Analytical Chemistry 74:5507–5512, 2002.
  2. Hickenbottom, S. J., Lemke, S. L., et al., Dual isotope test for assessing beta-caotene cleavage to vitamin A in humans. European Journal of Clinical Nutrition 41:141–147, 2002.
  3. Ognibene, T. J., Bench, G., et al., A new accelerator mass spectrometry system for 14C-quantification of biochemical samples. Journal of Mass Spectrometry and Ion Processes 218:255–264, 2002.
  4. Vogel, J. S., Grant, P. G., et al., Attomole quantitation of protein separations with accelerator mass spectrometry. Electrophoresis 22:2037–2045, 2001.
  5. Miyashita, M., Presley, J. M., et al., Attomole level protein sequencing by Edman degradation coupled with accelerator mass spectrometry. Proceedings of the National Academy of Sciences USA 98:4403–4408, 2001.
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National Resource for Mass Spectrometric Analysis of Biological Macromolecules
The Rockefeller University
1230 York Avenue
New York, NY 10021
http://prowl.rockefeller.edu

Grant No. P41 RR000862
Principal Investigator and Contact
Brian T. Chait, D.Phil.
212-327-8849; Fax: 212-327-7547
E-mail: chait@rockvax.rockefeller.edu

Research Emphasis

The resource develops new mass spectrometric (MS) 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 methodology 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 methodologies for studying protein phosphorylation: An 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 MS as a tool for the atomic resolution structure analysis of proteins, including integral membrane proteins and ion channels. Development of MS informatics tools for analysis of the proteome and tools for annotating the human genome using mass spectrometric information.

Resource Capabilities

Instruments

In-house constructed UV-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 LCMS and LCMS-MS of peptides; two in-house constructed MALDI-ion trap mass spectrometers utilizing Thermo-Finnigan LCQ instruments; prototype Sciex Centaur QqTOF tandem mass spectrometer in-house modified with a MALDI ion source sensitive MS and MS/MS of peptides.

Software

Publicly accessible mass spectrometry computer program/database is available at the website, along with a set of useful software tools (e.g., for protein identification spectrum manipulation, disulfide-mapping, etc.) 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.

  1. Cronshaw, J. M., Krutchinsky, A. N., et al., Proteomic analysis of the mammalian nuclear pore complex. Journal of Cell Biology 158:915–927, 2002.
  2. Krutchinsky, A. N. and Chait, B. T., On the nature of the chemical noise in MALDI mass spectra. Journal of American Society of Mass Spectrometry 13:129–134, 2002.
  3. Jiang, Y., Lee, A., Chen, J., et al., Crystal structure and mechanism of a calcium-gated potassium channel. Nature 417:515–522, 2002.
  4. Jiang, Y., Lee, A., Chen, J., Cadene, M., et al., The open pore conformation of potassium channels. Nature 417:523–526, 2002.
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Resource for Biomedical and Bio-organic Mass Spectrometry
Washington University
One Brookings Drive
St. Louis, MO 63130
http://wunmr.wustl.edu/~msf

Grant No. P41 RR000954
Principal Investigator: Chemistry
Michael L. Gross, Ph.D.
Department of Chemistry
314-935-4814; Fax: 314-935-7484
E-mail: mgross@wuchem.wustl.edu

Coprincipal Investigator: Biomedicine
John Turk, M.D., Ph.D.
Department of Medicine
314-362-8190; Fax: 314-362-8188
E-mail: jturk@imgate.wustl.edu

Research Emphasis

The focus of this resource is to provide access to state-of-the-art mass spectrometric (MS) instrumentation for researchers through collaborative research and service arrangements; to maintain a broad range of mass spectrometric instrumentation well-suited to studies of biomolecules; and to educate students in the mass spectrometric arts. A unique characteristic of this resource is dual facilities in the chemistry department and the medical school, both with an interactive staff.

Current Research

Instrument and method development in tandem quadrupole/time-of-flight, ion trap, and Fourier transform mass spectrometry (FTMS) are aims at the chemistry site. Structure determination of peptides, proteins, carcinogen-modified DNA fragments, and lipids are foci, as is H/D exchange for higher order structure of proteins. Studies of complex lipids and proteins and investigations using stable isotope tracer and complex are aims at the medical school site. Specific applications are the metabolism of proteins, glucose, and fatty acids, and the role of lipids in the biochemistry of insulin-producing cells.

Resource Capabilities

Instruments

Equipment at the chemistry site includes two Finnigan capillary LC/ion traps (LCQ), an ABI Voyager DE time-of-flight (TOF) mass spectrometer with matrix-assisted laser desorption ionization (MALDI), a new Micromass quadrupole/TOF tandem spectrometer equipped with electrospray ionization (ESI) and MALDI, FTMS instruments for instrument development, and three magnetic sectors including a unique four-sector tandem.

Equipment at the medical school site includes an ABI DE STR MALDI TOF (of the highest mass resolution for commercial MALDI instruments); a Finnigan LCQ ion-trap instrument with HPLC; TSQ 7000 triple quadrupole with ESI and HPLC; SSQ 7000 single-quadrupole GC/MS; and two Finnigan 3300 quadrupole, three Hewlett-Packard 5988 quadrupole, and two Hewlett-Packard 5970 quadrupole GC/mass spectrometers. The latter instruments are for high-sensitivity trace analysis using positive- and negative-ion chemical ionization. Equipment also includes a Finnigan isotope ratio instrument with online combustion and a bench-top Micromass QTOF with capillary HPLC.

Special Features

One research emphasis is tandem MS for studies of biomolecules. The resource’s complete array of tandem instruments permits collision-induced dissociation processes at both high and low energies. H/D exchange of proteins and structure determination of lipids are also focus efforts. The isotope tracer facility applies isotope ratio MS in metabolism studies and is the only NCRR resource with this capability.

  1. Hsu, F.-F. and Turk, J., Characterization of ceramides by low energy collisional-activated dissociation tandem mass spectrometry with negative-ion electrospray ionization. Journal of American Society of Mass Spectrometry 13:558–570, 2002.
  2. Suri, A., Vidavsky, I., et al., In APCs, the autologous peptides selected by the diabetogenic I-Ag7 molecule are unique and determined by the amino acid changes in the P9 pocket. Journal of Immunology 168:1235–1243, 2002.
  3. Chakravarti, D., Mailander, P. C., et al., Evidence that a burst of DNA depurination in SENCAR mouse skin induces error-prone repair and forms mutations in the H-ras gene. Oncogene 20:7945–7953, 2001.
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