High-sensitivity TFA-free LC-MS for profiling histones

Proteomics

Volumn 11, Issue 16, 2011, Pages 3326-3334

  You, Jia ^a   Wang, Liwen ^a   Saji, Motoyasu ^b   Olesik, Susan V ^a   Ringel, Matthew D ^b   Lucas, David M ^b   Byrd, John C ^b   Freitas, Michael A ^b  

^a OHIO STATE UNIVERSITY   (United States)

^b THE OHIO STATE UNIVERSITY COLLEGE OF MEDICINE   (United States)

Author keywords

Capillary nanoscale separation; Histone; RPLC MS; Technology; TFA free

Indexed keywords

ACETIC ACID; FORMIC ACID; HISTONE; TRIFLUOROACETIC ACID;

ARTICLE; CANCER CELL CULTURE; CHRONIC LYMPHATIC LEUKEMIA; HUMAN; HUMAN CELL; HUMAN CELL CULTURE; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PARTICLE SIZE; PRIMARY TUMOR; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN ANALYSIS;

ANIMALS; BREAST NEOPLASMS; CATTLE; CELL LINE, TUMOR; CHROMATOGRAPHY, LIQUID; FEMALE; FORMIC ACIDS; HISTONES; HUMANS; LEUKEMIA, LYMPHOCYTIC, CHRONIC, B-CELL; NANOTECHNOLOGY; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; TRIFLUOROACETIC ACID;

EID: 79960822249     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201000445     Document Type: Article

References (36)

1. Henry, K. W., Berger, S. L., Trans-tail histone modifications: wedge or bridge? Nat. Struct. Biol. 2002, 9, 565-566.
2. Inagaki, S., Nakamura, K., Morikami, A., A link among DNA replication, recombination, and gene expression revealed by genetic and genomic analysis of TEBICHI gene of Arabidopsis thaliana. PLoS Genet. 2009, 5, e1000613.
3. Edmondson, D. G., Davie, J. K., Zhou, J., Mirnikjoo, B. et al., Site-specific loss of acetylation upon phosphorylation of histone H3. J. Biol. Chem. 2002, 277, 29496-29502.
4. Lo, W. S., Trievel, R. C., Rojas, J. R., Duggan, L. et al., Phosphorylation of serine 10 in histone H3 is functionally linked in vitro and in vivo to Gcn5-mediated acetylation at lysine 14. Mol. Cell 2000, 5, 917-926.
5. Davie, J. K., Edmondson, D. G., Coco, C. B., Dent, S. Y., Tup1-Ssn6 interacts with multiple class I histone deacetylases in vivo. J. Biol. Chem. 2003, 278, 50158-50162.
6. Zhang, L., Freitas, M. A., Wickham, J., Parthun, M. R. et al., Differential expression of histone post-translational modifications in acute myeloid and chronic lymphocytic leukemia determined by high-pressure liquid chromatography and mass spectrometry. J. Am. Soc. Mass Spectrom. 2004, 15, 77-86.
7. Su, X., Jacob, N. K., Amunugama, R., Lucas, D. M. et al., Liquid chromatography mass spectrometry profiling of histones. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2007, 850, 440-454.
8. Zhang, K., Tang, H., Analysis of core histones by liquid chromatography-mass spectrometry and peptide mapping. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2003, 783, 173-179.
9. Bonenfant, D., Coulot, M., Towbin, H., Schindler, P., van Oostrum, J., Characterization of histone H2A and H2B variants and their post-translational modifications by mass spectrometry. Mol. Cell. Proteomics 2006, 5, 541-552.
10. Apffel, A., Fischer, S., Goldberg, G., Goodley, P. C., Kuhlmann, F. E., Enhanced sensitivity for peptide mapping with electrospray liquid chromatography-mass spectrometry in the presence of signal suppression due to trifluoroacetic acid-containing mobile phases. J. Chromatogr. A 1995, 712, 177-190.
11. Eshraghi, J., Chowdhury, S. K., Factors affecting electrospray ionization of effluents containing trifluoroacetic acid for high-performance liquid chromatography/mass spectrometry. Anal. Chem. 1993, 65, 3528-3533.
12. Duchateau, A. L. L., Munsters, B. H. M., Kwakkenbos, G. T. C., Van Leuken, R. G. J., Selection of buffers and of an ion-pairing agent for thermospray liquid chromatographic--mass spectrometric analysis of ionic compounds. J. Chromatogr. A 1991, 552, 605-612.
13. Clarke, N. J., Crow, F. W., Younkin, S., Naylor, S., Analysis of in vivo-derived amyloid-beta polypeptides by on-line two-dimensional chromatography-mass spectrometry. Anal. Biochem. 2001, 298, 32-39.
14. Chong, B. E., Yan, F., Lubman, D. M., Miller, F. R., Chromatofocusing nonporous reversed-phase high-performance liquid chromatography/electrospray ionization time-of-flight mass spectrometry of proteins from human breast cancer whole cell lysates: a novel two-dimensional liquid chromatography/mass spectrometry method. Rapid Commun. Mass Spectrom. 2001, 15, 291-296.
15. Garcia, M. C., The effect of the mobile phase additives on sensitivity in the analysis of peptides and proteins by high-performance liquid chromatography-electrospray mass spectrometry. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2005, 825, 111-123.
16. Cheson, B. D., Bennett, J. M., Grever, M., Kay, N. et al., National Cancer Institute-sponsored Working Group guidelines for chronic lymphocytic leukemia: revised guidelines for diagnosis and treatment. Blood 1996, 87, 4990-4997.
17. Debnath, J., Muthuswamy, S. K., Brugge, J. S., Morphogenesis and oncogenesis of MCF-10A mammary epithelial acini grown in three-dimensional basement membrane cultures. Methods 2003, 30, 256-268.
18. Sures, I., Gallwitz, D., Histone-specific acetyltransferases from calf thymus. Isolation, properties, and substrate specificity of three different enzymes. Biochemistry 1980, 19, 943-951.
19. Chadee, D. N., Hendzel, M. J., Tylipski, C. P., Allis, C. D. et al., Increased Ser-10 phosphorylation of histone H3 in mitogen-stimulated and oncogene-transformed mouse fibroblasts. J. Biol. Chem. 1999, 274, 24914-24920.
20. Garcia, M. C., Hogenboom, A. C., Zappey, H., Irth, H., Effect of the mobile phase composition on the separation and detection of intact proteins by reversed-phase liquid chromatography-electrospray mass spectrometry. J. Chromatogr. A 2002, 957, 187-199.
21. Nugent, K. D., Burton, W. G., Slattery, T. K., Johnson, B. F., Snyder, L. R., Separation of proteins by reversed-phase high-performance liquid chromatography. II. Optimizing sample pretreatment and mobile phase conditions. J. Chromatogr. 1988, 443, 381-397.
22. Kastner, M., Protein Liquid Chromatography, Elsevier, Amsterdam; NY 2000.
23. McCalley, D. V., Effect of buffer on peak shape of peptides in reversed-phase high performance liquid chromatography. J. Chromatogr. A 2004, 1038, 77-84.
24. Su, X., Lucas, D. M., Zhang, L., Xu, H. et al., Validation of an LC-MS based approach for profiling histones in chronic lymphocytic leukemia. Proteomics 2009, 9, 1197-1206.
25. Krokhin, O. V., Sequence-specific retention calculator. Algorithm for peptide retention prediction in ion-pair RP-HPLC: application to 300- and 100-A pore size C18 sorbents. Anal. Chem. 2006, 78, 7785-7795.
26. Ren, C., Zhang, L., Freitas, M. A., Ghoshal, K. et al., Peptide mass mapping of acetylated isoforms of histone H4 from mouse lymphosarcoma cells treated with histone deacetylase (HDACs) inhibitors. J. Am. Soc. Mass Spectrom. 2005, 16, 1641-1653.
27. Zhang, K., Williams, K. E., Huang, L., Yau, P. et al., Histone acetylation and deacetylation: identification of acetylation and methylation sites of HeLa histone H4 by mass spectrometry. Mol. Cell. Proteomics 2002, 1, 500-508.
28. Garcia, B. A., Mass spectrometric analysis of histone variants and post-translational modifications. Front Biosci. (Schol. Ed.) 2009, 1, 142-153.
29. Zee, B. M., Levin, R. S., Dimaggio, P. A., Garcia, B. A., Global turnover of histone post-translational modifications and variants in human cells. Epigenetics Chromatin 2010, 3, 22.
30. Phanstiel, D., Brumbaugh, J., Berggren, W. T., Conard, K. et al., Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells. Proc. Natl. Acad. Sci USA 2008, 105, 4093-4098.
31. Shechter, D., Nicklay, J. J., Chitta, R. K., Shabanowitz, J. et al., Analysis of histones in Xenopus laevis. I. A distinct index of enriched variants and modifications exists in each cell type and is remodeled during developmental transitions. J. Biol. Chem. 2009, 284, 1064-1074.
32. Nicklay, J. J., Shechter, D., Chitta, R. K., Garcia, B. A. et al., 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, 1075-1085.
33. Su, X., Jacob, N. K., Amunugama, R., Hsu, P. H. et al., Enrichment and characterization of histones by two-dimensional hydroxyapatite/reversed-phase liquid chromatography-mass spectrometry. Anal. Biochem. 2009, 388, 47-55.
34. Fraga, M. F., Ballestar, E., Villar-Garea, A., Boix-Chornet, M. et al., Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nat. Genet. 2005, 37, 391-400.
35. Lennartsson, A., Ekwall, K., Histone modification patterns and epigenetic codes. Biochim Biophys Acta 2009, 1790, 863-868.
36. Gupta, A., Guerin-Peyrou, T. G., Sharma, G. G., Park, C. et al., The mammalian ortholog of Drosophila MOF that acetylates histone H4 lysine 16 is essential for embryogenesis and oncogenesis. Mol. Cell. Biol. 2008, 28, 397-409.