University of California, San Francisco
521 Parnassus, Room 1124S
San Francisco, CA 94143-0446
Grant No. P41 RR001614
Investigator and Contact
A. L. Burlingame, Ph.D.
415-476-5641; Fax: 415-476-0688
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
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.
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.
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.
- 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 315:10631073, 2002.
- Greenbaum, D., Baruch, A., Hayrapetian, L., Darula, Z., Burlingame, A. L., et al., Chemical
approaches for functionally probing the proteome. Molecular Cellular Proteomics 1:6068, 2002.
- 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 1:930946, 2002.
- 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 1:500508, 2002.
Boston University School of Medicine
Departments of Biochemistry and Biophysics
715 Albany Street, R-806
Boston, MA 02118-2526
Grant No. P41 RR010888
Investigator and Contact
Catherine E. Costello, Ph.D.
617-638-6490; Fax: 617-638-6491
Joseph Zaia, Ph.D.
617-638-6762; Fax: 617-638-6761
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.
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.
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.
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.
- 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.
- 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 74:37603771, 2002.
- 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 13:402407, 2002.
- 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.
University of California
Lawrence Livermore National Laboratory
P.O. Box 808, L-452
7000 East Avenue
Livermore, CA 94551-0808
Grant No. P41 RR013461
Kenneth W. Turteltaub, Ph.D.
925-423-8152; Fax: 925-422-2282
925-422-6796; Fax: 925-422-8657
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
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.
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
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.
- Lu, C. M., Burton, D. W., Fitzgerald, R. L., et al., Mass spectrometric immunoassay for parathyroid
related protein. Analytical Chemistry 74:55075512, 2002.
- 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 41:141147, 2002.
- 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.
- Vogel, J. S., Grant, P. G., et al., Attomole quantitation of protein separations with accelerator
mass spectrometry. Electrophoresis 22:20372045, 2001.
- 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 98:44034408, 2001.
The Rockefeller University
1230 York Avenue
New York, NY 10021
Grant No. P41 RR000862
Investigator and Contact
Brian T. Chait, D.Phil.
212-327-8849; Fax: 212-327-7547
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.
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.
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.
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.
This combination of instruments allows rapid identification of proteins, elucidation of posttranslational
modification, determination of compactly folded protein domains, and determination of interactions between
- Cronshaw, J. M., Krutchinsky, A. N., et al., Proteomic analysis of the mammalian nuclear pore complex.
Journal of Cell Biology 158:915–927, 2002.
- 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.
- Jiang, Y., Lee, A., Chen, J., et al., Crystal structure and mechanism of a calcium-gated
potassium channel. Nature 417:515–522, 2002.
- Jiang, Y., Lee, A., Chen, J., Cadene, M., et al., The open pore conformation of potassium
channels. Nature 417:523–526, 2002.
One Brookings Drive
St. Louis, MO 63130
Grant No. P41 RR000954
Michael L. Gross, Ph.D.
Department of Chemistry
314-935-4814; Fax: 314-935-7484
Coprincipal Investigator: Biomedicine
John Turk, M.D., Ph.D.
Department of Medicine
314-362-8190; Fax: 314-362-8188
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.
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.
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.
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.
- 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.
- 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.
- 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.