Publications in 2009

One-pot shotgun quantitative mass spectrometry characterization of histones

Plazas-Mayorca, M.D.; Zee, B.M.; Young, N.L.; Fingerman, I.M.; LeRoy, G.; Briggs, S.D.; Garcia B.A., One-pot shotgun quantitative mass spectrometry characterization of histones. Journal of Proteome Research, 2009, 8, 1), 67-74.

A mixed-integer linear optimization framework for the identification and quantification of targeted post-translational modifications of highly modified proteins using multiplexed ETD tandem mass spectrometry

Dimaggio, P. A.; Young, N. L.; Baliban, R. C.; Garcia, B. A.; Floudas, C. A., A mixed-integer linear optimization framework for the identification and quantification of targeted post-translational modifications of highly modified proteins using multiplexed ETD tandem mass spectrometry . Mol Cell Proteomics 2009, 8, 2527.43.

Protein quantification across hundreds of experimental conditions

Khan, Z.; Bloom, J.S.; Garcia, B.A.; Singh, M.; Krugylak, L., Protein quantification across hundreds of experimental conditions. PNAS, 2009, 106, (37),15544-8.

High-throughput characterization of combinatorial histone codes

Young, N. L.; Dimaggio, P. A.; Plazas-Mayorca, M. D.; Baliban, R. C.; Floudas, C. A.; Garcia, B. A., High-throughput characterization of combinatorial histone codes. Mol Cell Proteomics, 2009, 8, (10), 2266-84. (*High-lighted as a Faculty of 1000 Must read article, http://f1000biology.com/article/id/1164285/evaluation)

Proteome-wide prediction of acetylation substrates

Basu, A.; Rose, K.L.; Zhang, J.; Beavis, R.C.; Ueberheide, B.; Garcia, B.A.; Chait, B.T.; Zhao, Y.; Hunt, D.F.; Segal, E.; Allis, C.D.; Hake, S.B., Proteome-wide prediction of acetylation substrates. PNAS, 2009, 106, (33), 13785-90.

Heterochromatin protein 1 is extensively decorated with histone code-like post-translational modifications

Leroy, G.; Weston, J. T.; Zee, B. M.; Young, N. L.; Plazas-Mayorca, M. D.; Garcia, B. A., Heterochromatin protein 1 is extensively decorated with histone code-like post-translational modifications. Mol Cell Proteomics, 2009, 8, 2432-42.

Decoding the histone code by quantitative proteomics

Leroy, G.; Plazas-Mayorca, M. D.; Young, N. L.; Garcia, B. A., Decoding the histone code by quantitative proteomics. Mol Cell Proteomics, 8, (8), Supplement 1, S11, 2009.

Histone H3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells

Xie, W.; Song, C.; Young, N. L.; Sperling, A. S.; Xu, F.; Sridharan, R.; Conway, A. E.; Garcia, B. A.; Plath, K.; Clark, A. T.; Grunstein, M., Histone H3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells. Mol Cell 2009, 33, (4), 417-27.

Mass spectrometric analysis of histone variants and post-translational modifications

Garcia, B. A., Mass spectrometric analysis of histone variants and post-translational modifications. Front Biosci (Schol Ed) 2009, 1, 142-53.

Chromatin-specific remodeling by HMGB1 and linker histone H1 silences proinflammatory genes during endotoxin tolerance

El Gazzar, M.; Yoza, B. K.; Chen, X.; Garcia, B. A.; Young, N. L.; McCall, C. E., Chromatin-specific remodeling by HMGB1 and linker histone H1 silences proinflammatory genes during endotoxin tolerance. Mol Cell Biol 2009, 29, (7), 1959-71.

Identification of differentially expressed histone codes by mass spectrometry

Plazas-Mayorca, M.D.; N.L. Young, N.L.; Garcia B.A., Identification of differentially expressed histone codes by mass spectrometry, American Biotechnology Laboratory Journal, 2009, 27(2), 10-12.

A method to separate and characterize modified forms of histones using cation-exchange HILIC chromatography and electron transfer dissociation-mass spectrometry

Young, N.L.; Plazas-Mayorca, M.D.; Garcia, B.A., A method to separate and characterize modified forms of histones using cation-exchange HILIC chromatography and electron transfer dissociation-mass spectrometry, American Biotechnology Laboratory Journal, 2009, 27(1), 23-25.

nalysis of histones in Xenopus laevis. II. mass spectrometry reveals an index of cell type-specific modifications on H3 and H4

Nicklay, J. J.; Shechter, D.; Chitta, R. K.; Garcia, B. A.; Shabanowitz, J.; Allis, C. D.; Hunt, D. F., Analysis of histones in Xenopus laevis. II. mass spectrometry reveals an index of cell type-specific modifications on H3 and H4. J Biol Chem 2009, 284, (2), 1075-85.

Tandem mass spectrometry with ultrahigh mass accuracy clarifies peptide identification by database retrieval

Boyne, M. T.; Garcia, B. A.; Li, M.; Zamdborg, L.; Wenger, C. D.; Babai, S.; Kelleher, N. L., Tandem mass spectrometry with ultrahigh mass accuracy clarifies peptide identification by database retrieval. J Proteome Res 2009, 8, (1), 374-9.