The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Proteomic and phosphoproteomic comparison of human ES and iPS cells
Open accessAbstract
Combining high-mass-accuracy mass spectrometry, isobaric tagging and software for multiplexed, large-scale protein quantification, we report deep proteomic coverage of four human embryonic stem cell and four induced pluripotent stem cell lines in biological triplicate. This 24-sample comparison resulted in a very large set of identified proteins and phosphorylation sites in pluripotent cells. The statistical analysis afforded by our approach revealed subtle but reproducible differences in protein expression and protein phosphorylation between embryonic stem cells and induced pluripotent cells. Merging these results with RNA-seq analysis data, we found functionally related differences across each tier of regulation. We also introduce the Stem Cell–Omics Repository (SCOR), a resource to collate and display quantitative information across multiple planes of measurement, including mRNA, protein and post-translational modifications.
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Cites
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells
Yu, J., Vodyanik, M. A., Smuga-Otto, K., Antosiewicz-Bourget, J., Frane, J. L., Tian, S., Nie, J., Jonsdottir, G. A., Ruotti, V., Stewart, R., et al. (2007) · Science · doi:10.1126/science.1151526 · Cited by 10,310
Self-citationRoss, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., et al. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m400129-mcp200 · Cited by 4,401
Derivation of human embryonic stem cells in defined conditions
Ludwig, T. E., Levenstein, M. E., Jones, J. M., Berggren, W. T., Mitchen, E. R., Frane, J. L., Crandall, L. J., Daigh, C. A., Conard, K. R., Piekarczyk, M. S., et al. (2006) · Nature Biotechnology · doi:10.1038/nbt1177 · Cited by 1,114
Self-citationInterpretation of Shotgun Proteomic Data
Nesvizhskii, A. I., & Aebersold, R. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r500012-mcp200 · Cited by 1,025
A dual pressure linear ion trap orbitrap instrument with very high sequencing speed
Olsen, J. V., Schwartz, J. C., Griep-Raming, J., Nielsen, M. L., Damoc, E., Denisov, E., Lange, O., Remes, P., Taylor, D., Splendore, M., et al. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900375-mcp200 · Cited by 464
Cited by
Comet: An open‐source MS / MS sequence database search tool
Eng, J. K., Jahan, T. A., & Hoopmann, M. R. (2013) · PROTEOMICS · doi:10.1002/pmic.201200439 · Cited by 1,474
EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments
Leng, N., Dawson, J. A., Thomson, J. A., Ruotti, V., Rissman, A. I., Smits, B. M. G., Haag, J. D., Gould, M. N., Stewart, R. M., & Kendziorski, C. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt087 · Cited by 1,302
Self-citationPINK1 phosphorylates ubiquitin to activate Parkin E3 ubiquitin ligase activity
Kane, L. A., Lazarou, M., Fogel, A. I., Li, Y., Yamano, K., Sarraf, S. A., Banerjee, S., & Youle, R. J. (2014) · Journal of Cell Biology · doi:10.1083/jcb.201402104 · Cited by 1,298
Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome
Hebert, A. S., Dittenhafer-Reed, K. E., Yu, W., Bailey, D. J., Selen, E. S., Boersma, M. D., Carson, J. J., Tonelli, M., Balloon, A. J., Higbee, A. J., et al. (2013) · Molecular Cell · doi:10.1016/j.molcel.2012.10.024 · Cited by 636
Self-citationIncreasing the Multiplexing Capacity of TMTs Using Reporter Ion Isotopologues with Isobaric Masses
McAlister, G. C., Huttlin, E. L., Haas, W., Ting, L., Jedrychowski, M. P., Rogers, J. C., Kuhn, K., Pike, I., Grothe, R. A., Blethrow, J. D., et al. (2012) · Analytical Chemistry · doi:10.1021/ac301572t · Cited by 605
Metadata
- Authors
- Phanstiel, D. H., Brumbaugh, J., Wenger, C. D., Tian, S., Probasco, M. D., Bailey, D. J., Swaney, D. L., Tervo, M. A., Bolin, J. M., Ruotti, V., Stewart, R., Thomson, J. A., & Coon, J. J.
- Venue
- Nature Methods
- Published
- 2011-09-11
- Volume
- 8
- Issue
- 10
- Pages
- 821-827
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2096217402
- Cited by
- 259
- References
- 6
- FWCI
- 16.82
- Type
- journal article
- Language
- en
- Open access
- green
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- Phanstiel, D. H., Brumbaugh, J., Wenger, C. D., Tian, S., Probasco, M. D., Bailey, D. J., Swaney, D. L., Tervo, M. A., Bolin, J. M., Ruotti, V., Stewart, R., Thomson, J. A., & Coon, J. J. (2011). Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nature Methods. https://doi.org/10.1038/nmeth.1699
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