Suggested Topics for Discussion in 523b
Mass Spectrometry
1. Protein Folding and Proteome dynamics
Robinson EW, Williams ER. Multidimensional separations of ubiquitin conformers in the
gas phase: relating ion cross sections to h/d exchange measurements. J Am Soc Mass
Spectrom. 2005 Sep;16(9):1427-37
Hydrogen exchange mass spectrometry for the analysis of protein dynamics
Wales, Thomas E.; Engen, John R. Mass Spec Reviews 2005 pp. 158 – 170
Wintrode PL, Rojsajjakul T, Vadrevu R, Matthews CR, Smith DL. An obligatory
intermediate controls the folding of the alpha-subunit of tryptophan synthase, a TIM
barrel protein. J Mol Biol. 2005 Apr 15;347(5):911-9
2. Detection of virus by mass ppectrometry
Bothner B, Siuzdak G. Electrospray Ionization of a Whole Virus : Analyzing Mass,
Structure, and Viability. ChemBiochem 2004 5, 258-260.
Bothner B, Taylor DJ, Jun B, Lee KK, Siuzdak G, Schultz CP, Johnson JE. Maturation of
a tetravirus capsid alters the dynamic properties and creates a metastable complex.
Virology 2005 334(1):17-27.
3. Macromolecular complexes
Divakaruni AV, Loo RR, Xie Y, Loo JA, Gober JW. The cell-shape protein MreC
interacts with extracytoplasmic proteins including cell wall assembly complexes in
Caulobacter crescentus. Proc Natl Acad Sci U S A. 2005 Dec 20;102(51):18602-7.
Ilag LL, Videler H, McKay AR, Sobott F, Fucini P, Nierhaus KH, Robinson CV.
Heptameric (L12)6/L10 rather than canonical pentameric complexes are found by tandem
MS of intact ribosomes from thermophilic bacteria. Proc Natl Acad Sci U S A. 2005 Jun
7;102(23):8192-7
Videler H, Ilag LL, McKay AR, Hanson CL, Robinson CV. Mass spectrometry of intact
ribosomes. FEBS Lett. 2005 Feb 7;579(4):943-7
Kerner MJ, Naylor DJ, Ishihama Y, Maier T, Chang HC, Stines AP, Georgopoulos C,
Frishman D, Hayer-Hartl M, Mann M, Hartl FU. Proteome-wide analysis of chaperonindependent protein folding in Escherichia coli. Cell. 2005 Jul 29;122(2):209-20.
Talkington MW, Siuzdak G, Williamson JR. Related Articles, Links An assembly
landscape for the 30S ribosomal subunit.
Nature. 2005 Dec 1;438(7068):628-32.
4. Protein-Protein Interaction
Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A,
Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A.
Interaction network containing conserved and essential protein complexes in Escherichia
coli. Nature. 2005 Feb 3;433(7025):531-7.
Schulze WX, Mann M. A novel proteomic screen for peptide-protein interactions.
J Biol Chem. 2004 Mar 12;279(11):10756-64
Jager M, Michalet X, Weiss S. Protein-protein interactions as a tool for site-specific
labeling of proteins. Protein Sci. 2005 Aug;14(8):2059-68
5. Tissue Imaging
Reyzer ML, Caprioli RM. MALDI mass spectrometry for direct tissue analysis: a new
tool for biomarker discovery. J Proteome Res. 2005 Jul-Aug;4(4):1138-42.
Caldwell RL, Caprioli RM. Tissue profiling by mass spectrometry: a review of
methodology and applications. Mol Cell Proteomics. 2005 Apr;4(4):394-401.
6. Proteomics
Andersen JS, Lam YW, Leung AK, Ong SE, Lyon CE, Lamond AI, Mann M.
Nucleolar proteome dynamics. Nature. 2005 Jan 6;433(7021):77-83.
Andersen JS, Wilkinson CJ, Mayor T, Mortensen P, Nigg EA, Mann M. Proteomic
characterization of the human centrosome by protein correlation profiling.
Nature. 2003 Dec 4;426(6966):570-4
7. Metabolomics
Ippolito JE, Xu J, Jain S, Moulder K, Mennerick S, Crowley JR, Townsend RR, Gordon
JI. Related Articles, Links An integrated functional genomics and metabolomics
approach for defining poor prognosis in human neuroendocrine cancers.
Proc Natl Acad Sci U S A. 2005 Jul 12;102(28):9901-6.
Dunn WB, Bailey NJ, Johnson HE. Measuring the metabolome: current analytical
technologies. Analyst. 2005 May;130(5):606-25
8. Biomarkers
Anderson NL, Anderson NG, Haines LR, Hardie DB, Olafson RW, Pearson TW.
Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards
and Capture by Anti-Peptide Antibodies (SISCAPA).
J Proteome Res. 2004 Mar-Apr;3(2):235-44.
Roesli C, Elia G, Neri D. Two-dimensional mass spectrometric mapping.
Curr Opin Chem Biol. 2006 Jan 4;
9. Small molecules Screening
Ilag LL, Ubarretxena-Belandia I, Tate CG, Robinson CV
Drug binding revealed by tandem mass spectrometry of a protein-micelle complex.
J Am Chem Soc. 2004 Nov 10;126(44):14362-3.
Deng G, Sanyal G. Applications of mass spectrometry in early stages of target based
drug discovery. J Pharm Biomed Anal. 2005 Oct 24;
Ng ES, Yang F, Kameyama A, Palcic MM, Hindsgaul O, Schriemer DC.
High-throughput screening for enzyme inhibitors using frontal affinity chromatography
with liquid chromatography and mass spectrometry.
Anal Chem. 2005 Oct 1;77(19):6125-33
10. Top-down sequencing with FT ICR
Jebanathirajah JA, Pittman JL, Thomson BA, Budnik BA, Kaur P, Rape M, Kirschner M,
Costello CE, O'connor PB. Characterization of a New qQq-FTICR Mass Spectrometer
for Post-Translational Modification Analysis and Top-Down Tandem Mass Spectrometry
of Whole Proteins. J Am Soc Mass Spectrom. 2005 Dec;16(12):1985-99.
Ge Y, Lawhorn BG, ElNaggar M, Strauss E, Park JH, Begley TP, McLafferty FW. Topdown characterization of larger proteins (45 kDa) by electron capture dissociation mass
spectrometry. J Am Chem Soc. 2002 Jan 30;124(4):672-8.
Kelleher NL. Top-down proteomics.
Anal Chem. 2004 Jun 1;76(11):197A-203A.
11. Enzyme Mechanism
Garneau S, Dorrestein PC, Kelleher NL, Walsh CT. Characterization of the formation of
the pyrrole moiety during clorobiocin and coumermycin A1 biosynthesis. Biochemistry.
2005 Mar 1;44(8):2770-80.
McLoughlin SM, Kelleher NL. Kinetic and regiospecific interrogation of covalent
intermediates in the nonribosomal peptide synthesis of yersiniabactin.
J Am Chem Soc. 2004 Oct 20;126(41):13265-75.
12. Ion Mobility
Venne K, Bonneil E, Eng K, Thibault P.
Improvement in peptide detection for proteomics analyses using NanoLC-MS and highfield asymmetry waveform ion mobility mass spectrometry.
Anal Chem. 2005 Apr 1;77(7):2176-86
Loo JA, Berhane B, Kaddis CS, Wooding KM, Xie Y, Kaufman SL, Chernushevich IV.
Electrospray ionization mass spectrometry and ion mobility analysis of the 20S
proteasome complex. J Am Soc Mass Spectrom. 2005 Jul;16(7):998-1008
13. Other