Proteins & Mass Spectrometry
Mass spectrometry and tandem MS/MS
Bibliography (Available in C1734
for reading, copying)
Books:
Burlingame, A. L., S. A. Carr, M.A. Baldwin (2000).
Mass Spectrometry In Biology & Medicine. Totowa, N.J.,
Humana Press.
Chapman, J. R., Ed. (1996). Protein And Peptide
Analysis By Mass Spectrometry. Methods in Molecular
Biology. Totowa, NJ, Humana Press.
Hancock, W. S., Ed. (1996). New Methods In Peptide
Mapping For The Characterization Of Proteins. CRC Series
in Analytical Chemistry. Boca Raton, FL, CRC Press.
Lee, T. A. (1998). A Beginner's Guide To Mass
Spectral Interpretation. West Sussex, England, John Wiley
& Sons.
Rabilloud, T., Ed. (2000). Proteome Research:
Two-Dimensional Gel Electrophoresis And Identification
Methods. Berlin, Springer Verlag.
Siuzdak, G. (1996). Mass Spectrometry For
Biotechnology. San Diego, Calif., Academic Press.
Sparkman, O. D. (2000). Mass Spectrometry Desk
Reference. Pittsburgh, PA, Global View Publishing.
Wilkins, M. R., K. L. Williams, R.D. Appel, D.F.
Hochstrasser, Eds. (1997). Proteome Research: New
Frontiers In Functional Genomics. Berlin, Springer-Verlag.
Journal Articles (Available in C1734):
Introduction to and comparison of different Mass
Spec methods; general proteomics:
Andersen, J. S., B. Svensson, et al. (1996). Electrospray
ionization and matrix assisted laser desorption/ionization
mass spectrometry: powerful analytical tools in
recombinant protein chemistry. Nat Biotechnol 14(4):
449-57.
Chapman, J. R. (1996). Mass Spectometry:
Ionization methods and instrumentation. Protein and
peptide analysis by mass spectrometry. C. J. R. Totowa,
NJ, Humana Press. 61: 9-28.
Gillece-Castro, B. L. and J. T. Stults (1996). Peptide
characterization by mass spectrometry. Methods
Enzymol 271: 427-48.
Hillenkamp, F. and M. Karas (1990). Mass
spectrometry of peptides and proteins by matrix-assisted
ultraviolet laser desorption/ionization. Methods
Enzymol 193: 280-95.
Karas, M. and U. Bahr (1993). Laser desorption
ionization mass spectrometry of bioorganic molecules.
Spectroscopic Methods and Analyses: NMR, Mass
Spectrometry, and Metalloprotein Techniques. C. Jones,
B. Mulloy and A. H. Thomas. Totowa, NJ, Humana Press.
17: 215-228.
Karas, M. (1996). Matrix-assisted laser
desorption ionization MS: a progress report.
Biochem Soc Trans 24(3): 897-900.
Moore, W. T. (1997). Laser desorption mass
spectrometry. Methods Enzymol 289: 520-42.
Vestal, M. L., P. Juhasz, et al. (1995). Delayed
extraction matrix-assisted laser desorption
time-of-flight mass spectrometry. Rapid Commun Mass
Spectrom 9: 1044-1050.
Wait, R. (1993). Introduction to mass
spectrometry. Spectroscopic methods and analysis:
NMR, mass spectrometry, and metalloprotein techniques.
C. Jones, B. Mulloy and A. H. Thomas. Totowa, NJ, Humana
Press. 17: 191-213.
MALDI from SDS PAGE gels, Blots, TLC Plates;
Tryptic/other Digests; Protein elution from Gels, blots:
Cohen, S. L. and B. T. Chait (1997). Mass
spectrometry of whole proteins eluted from sodium
dodecyl sulfate- polyacrylamide gel electrophoresis gels.
Anal Biochem 247(2): 257-67.
Cottrell, J. S. and C. W. Sutton (1996). The
identification of electrophoretically separated proteins
by peptide mass fingerprinting. Protein and peptide
analysis by mass spectrometry. J. R. Chapman. Totowa,
N.J., Humana Press. 61: 67-82.
Fernandez, J., F. Gharahdaghi, et al. (1998). Routine
identification of proteins from sodium dodecyl sulfate-
polyacrylamide gel electrophoresis (SDS-PAGE) gels or
polyvinyl difluoride membranes using matrix assisted
laser desorption/ionization- time of flight-mass
spectrometry (MALDI-TOF-MS). Electrophoresis 19(6):
1036-45.
Jensen, O. N., M. R. Larsen, et al. (1998). Mass
spectrometric identification and microcharacterization
of proteins from electrophoretic gels: Strategies and
applications. Proteins Suppl. 2: 74-79.
Jimιnez, C. R., L. Huang, et al. (1998). In-gel
digestion of proteins for MALDI-MS fingerprint mapping.
Current protocols in Protein Science, John Wiley & Sons:
16.4.1-16.4.5.
Krause, E., H. Wenschuh, et al. (1999). The
dominance of arginine-containing peptides in MALDI-derived
tryptic mass fingerprints of proteins. Anal Chem
71(19): 4160-5.
Kussmann, M., U. Lassing, et al. (1997). Matrix-assisted
laser desorption/ionization mass spectrometric peptide
mapping of the neural cell adhesion protein neurolin
purified by sodium dodecyl sulfate polyacrylamide gel
electrophoresis or acidic precipitation. J Mass
Spectrom 32(5): 483-93.
Lui, M., P. Tempst, et al. (1996). Methodical
analysis of protein-nitrocellulose interactions to
design a refined digestion protocol. Anal Biochem
241(2): 156-66.
Mehl, J. T., A. J. Nicola, et al. (1998). Direct
coupling of thin-layer chromatography with
matrix-assisted laser desorption/ionization mass
spectrometry. American Laboratory: 30-38.
Schey, K. L. (1996). Hydrophobic proteins and
peptides analyzed by matrix-assisted laser desorption/ionization.
Protein and Peptide Analysis by Mass Spectrometry. J. R.
Chapman. Totowa, NJ, Humana Press, Inc. 61:
227-230.
Speicher, K. D., O. Kolbas, et al. (2000). Systematic
analysis of peptide recoveries from in-gel digestions
for protein identification in proteome studies.
Journal of Biomolecular Techniques 11(2): 74-86.
Xiang, F. and R. C. Beavis (1993). Growing
protein-doped sinapinic acid crystals for laser
desorption: An alternative preparation method for
difficult samples. Organic Mass Spectrometry 28:
1424-1429.
Phosphopeptide Analysis:
Annan, R. S. and S. A. Carr (1997). The
essential role of mass spectrometry in characterizing
protein structure: mapping posttranslational
modifications. J Protein Chem 16(5):
391-402.
Mitchellhill, K. (1999). Phosphorylation Site
Analysis., ABRF Web site www.abrf.org
Neubauer, G. and M. Mann (1999). Mapping of
phosphorylation sites of gel-isolated proteins by
nanoelectrospray tandem mass spectrometry: potentials
and limitations. Anal Chem 71(1): 235-42.
Oda, Y., K. Huang, F. R. Cross, D. Cowburn and B.
T. Chait (1999). Accurate quantitation of protein
expression and site-specific phosphorylation. Proc
Natl Acad Sci U S A 96(12): 6591-6.
Resing, K. (1999). Phosphorylation site
analysis with iron chelation chromatography., ABRF
Web site www.abrf.org
Peptide Sequencing by Mass Spec:
Katta, V., D. T. Chow, et al. (1998). Applications
of in-source fragmentation of protein ions for direct
sequence analysis by delayed extraction MALDI-TOF mass
spectrometry. Anal Chem 70(20): 4410-6.
Patterson, D. H., G. E. Tarr, et al. (1995). C-terminal
ladder sequencing via matrix-assisted laser desorption
mass spectrometry coupled with carboxypeptidase Y
time-dependent and concentration-dependent digestions.
Anal Chem 67(21): 3971-8.
Wang, R. and B. T. Chait (1996).
Posttranslational modifications analyzed by automated
protein ladder sequencing. Protein and peptide
analysis by mass spectrometry. J. R. Chapman. Totowa,
NJ, Humana Press. 61: 161-170.
DNA, oligonucleotide Sequence Analysis by MALDI:
Haff, L. A. and I. P. Smirnov (1996). DNA
sequence analysis by matrix-assisted laser desorption
ionization MS. Biochem Soc Trans 24(3):
901-4.
Roskey, M. T., P. Juhasz, et al. (1996). DNA
sequencing by delayed extraction-matrix-assisted laser
desorption/ionization time of flight mass spectrometry.
Proc Natl Acad Sci U S A 93(10): 4724-9.
Smirnov, I. P., M. T. Roskey, et al. (1996). Sequencing
oligonucleotides by exonuclease digestion and delayed
extraction matrix-assisted laser desorption ionization
time-of-flight mass spectrometry. Anal Biochem
238(1): 19-25.
Glycoprotein & Oligosaccharide Analysis by Mass
Spec:
Hancock, W. S., A. Apffel, et al. (1996). Reversed-phase
peptide mapping of glycoproteins using liquid
chromatography/electrospray ionization-mass spectrometry.
Methods Enzymol 271: 403-27.
Harvey, D. J. (1996). Identification of cleaved
oligosaccharides by matrix-assisted laser desorption/ionization.
Protein and Peptide Analysis by Mass Spectrometry. J. R.
Chapman. Totowa, NJ, Humana Press. 61: 243-253.
Harvey, D. J., T. J. Naven, et al. (1996). Identification
of oligosaccharides by matrix-assisted laser desorption
ionization and electrospray MS. Biochem Soc Trans
24(3): 905-12.
Oliver, R. W., B. N. Green, et al. (1996). The
use of electrospray ionization MS to determine the
structure of glycans in intact glycoproteins.
Biochem Soc Trans 24(3): 917-27.
Miscellaneous MALDI Analyses (SNPs with PNA;
Noncovalently bound compounds):
Ross, P. L., K. Lee, et al. (1997). Discrimination
of single-nucleotide polymorphisms in human DNA using
peptide nucleic acid probes detected by MALDI-TOF mass
spectrometry. Anal Chem 69(20): 4197-202.
Woods, A. S., J. C. Buchsbaum, et al. (1995). Matrix-assisted
laser desorption/ionization of noncovalently bound
compounds. Anal Chem 67(24): 4462-4465.
Protein Methods (Concentration of proteins; 2D
gel information):
Aguilar, R. M., J. J. Bustamante, et al. (1999). Precipitation
of dilute chromatographic samples (ng/ml) containing
interfering substances for SDS-PAGE. Anal Biochem
267(2): 344-50.
Celis, J. E. and P. Gromov (1999). 2D protein
electrophoresis: can it be perfected? Curr Opin
Biotechnol 10(1): 16-21.
Ziegler, J., T. Vogt, et al. (1997). Concentration
of dilute protein solutions prior to sodium dodecyl
sulfate-polyacrylamide gel electrophoresis. Anal
Biochem 250(2): 257-60.
Database Searching with Mass Spec information:
Oliver, R. W. and M. P. Carrier (1996). The
use of databases in searching the literature of
biological mass spectrometry. Methods Mol Biol
61: 295-309.
Electrospray Ionization Mass Spec (ESI):
Covey, T. (1996). Liquid chromatography/mass
spectrometry for the analysis of protein digests.
Methods Mol Biol 61: 83-99.
Ducret, A., I. Van Oostveen, et al. (1998). High
throughput protein characterization by automated
reverse-phase chromatography/electrospray tandem mass
spectrometry. Protein Sci 7(3): 706-19.
Fearnley, I. M. and J. E. Walker (1996). Analysis
of hydrophobic proteins and peptides by electrospray
ionization MS. Biochem Soc Trans 24(3):
912-7.
Yates, J. R. (1996). Protein structure
analysis by mass spectrometry. Methods Enzymol
271: 351-77.
Other Mass Spec techniques (FAB, Plasma
Desorption; FTIR MS):
Costello, C. E. (1993). Tandem Mass
Spectrometry. Spectroscopic methods and analyses:
NMR, mass spectrometry, and metalloproteins. C. Jones,
B. Mulloy and A. H. Thomas. Totowa, NJ, Humana Press.
17: 285-313.
Roepstorff, P. (1993). 252-Californium plasma
desorption time-of-flight mass spectrometry of peptides
and proteins. Meth Molecular Biology 17:
229-235.
Wait, R. (1993). Fast atom bombardment mass
spectrometry of peptides. Spectroscopic methods and
analyses: NMR, mass spectrometry, and metalloproteins.
C. Jones, B. Mulloy and A. H. Thomas. Totowa, NJ, Humana
Press. 17: 237-283.
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