The DOI matches its Crossref record; 58 of the 58 references it cites were found in a registry or an index.
The quantitative and condition-dependent Escherichia coli proteome
Open accessAbstract
Measuring precise concentrations of proteins can provide insights into biological processes. Here we use efficient protein extraction and sample fractionation, as well as state-of-the-art quantitative mass spectrometry techniques to generate a comprehensive, condition-dependent protein-abundance map for Escherichia coli. We measure cellular protein concentrations for 55% of predicted E. coli genes (>2,300 proteins) under 22 different experimental conditions and identify methylation and N-terminal protein acetylations previously not known to be prevalent in bacteria. We uncover system-wide proteome allocation, expression regulation and post-translational adaptations. These data provide a valuable resource for the systems biology and broader E. coli research communities.
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Cites
Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection
Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., & Mori, H. (2006) · Molecular Systems Biology · doi:10.1038/msb4100050 · Cited by 7,858
UniProt: the Universal Protein knowledgebase
Apweiler, R. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh131 · Cited by 7,498
The Complete Genome Sequence of Escherichia coli K-12
Blattner, F. R., Plunkett, G., Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., et al. (1997) · Science · doi:10.1126/science.277.5331.1453 · Cited by 7,452
Global quantification of mammalian gene expression control
Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566
Keller, A., Nesvizhskii, A. I., Kolker, E., & Aebersold, R. (2002) · Analytical Chemistry · doi:10.1021/ac025747h · Cited by 4,830
Self-citationThe COG database: an updated version includes eukaryotes
Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S. L., Nikolskaya, A. N., et al. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-41 · Cited by 4,430
TANDEM: matching proteins with tandem mass spectra
Craig, R., & Beavis, R. C. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth092 · Cited by 2,536
The Proteomics Identifications (PRIDE) database and associated tools: status in 2013
Vizcaíno, J. A., Côté, R. G., Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., Griss, J., Alpi, E., Birim, M., Contell, J., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1262 · Cited by 1,918
Expanded microbial genome coverage and improved protein family annotation in the COG database
Galperin, M. Y., Makarova, K. S., Wolf, Y. I., & Koonin, E. V. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1223 · Cited by 1,572
Absolute Quantification of Proteins by LCMSE
Silva, J. C., Gorenstein, M. V., Li, G.-Z., Vissers, J. P. C., & Geromanos, S. J. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500230-mcp200 · Cited by 1,529
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The world of protein acetylation
Drazic, A., Myklebust, L. M., Ree, R., & Arnesen, T. (2016) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2016.06.007 · Cited by 804
iML1515, a knowledgebase that computes Escherichia coli traits
Monk, J. M., Lloyd, C. J., Brunk, E., Mih, N., Sastry, A., King, Z., Takeuchi, R., Nomura, W., Zhang, Z., Mori, H., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3956 · Cited by 560
Davidi, D., Noor, E., Liebermeister, W., Bar-Even, A., Flamholz, A., Tummler, K., Barenholz, U., Goldenfeld, M., Shlomi, T., & Milo, R. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1514240113 · Cited by 266
Heckmann, D., Lloyd, C. J., Mih, N., Ha, Y., Zielinski, D. C., Haiman, Z. B., Desouki, A. A., Lercher, M. J., & Palsson, B. O. (2018) · Nature Communications · doi:10.1038/s41467-018-07652-6 · Cited by 218
Nielsen, J. (2017) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-061516-044757 · Cited by 252
Metadata
- Authors
- Schmidt, A., Kochanowski, K., Vedelaar, S., Ahrné, E., Volkmer, B., Callipo, L., Knoops, K., Bauer, M., Aebersold, R., & Heinemann, M.
- Venue
- Nature Biotechnology
- Published
- 2016-01
- Volume
- 34
- Issue
- 1
- Pages
- 104-110
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2191824721
- Cited by
- 771
- References
- 58
- FWCI
- 23.77
- Type
- journal article
- Language
- en
- Open access
- bronze
- Licence
- www.springer.com/tdm (tdm)
- www.springer.com/tdm (vor)
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- Schmidt, A., Kochanowski, K., Vedelaar, S., Ahrné, E., Volkmer, B., Callipo, L., Knoops, K., Bauer, M., Aebersold, R., & Heinemann, M. (2016). The quantitative and condition-dependent Escherichia coli proteome. Nature Biotechnology. https://doi.org/10.1038/nbt.3418
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