The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation
Open accessAbstract
In-depth MS-based proteomics has necessitated fractionation of either proteins or peptides or both, often requiring considerable analysis time. Here we employ long liquid chromatography runs with high resolution coupled to an instrument with fast sequencing speed to investigate how much of the proteome is directly accessible to liquid chromatography-tandem MS characterization without any prefractionation steps. Triplicate single-run analyses identified 2990 yeast proteins, 68% of the total measured in a comprehensive yeast proteome. Among them, we covered the enzymes of the glycolysis and gluconeogenesis pathway targeted in a recent multiple reaction monitoring study. In a mammalian cell line, we identified 5376 proteins in a triplicate run, including representatives of 173 out of 200 KEGG metabolic and signaling pathways. Remarkably, the majority of proteins could be detected in the samples at sub-femtomole amounts and many in the low attomole range, in agreement with absolute abundance estimation done in previous works (Picotti et al. Cell, 138, 795-806, 2009). Our results imply an unexpectedly large dynamic range of the MS signal and sensitivity for liquid chromatography-tandem MS alone. With further development, single-run analysis has the potential to radically simplify many proteomic studies while maintaining a systems-wide view of the proteome.
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Citations
Cites
Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855
Self-citationMass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955
Self-citationGlobal analysis of protein localization in budding yeast
Huh, W.-K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S., & O'Shea, E. K. (2003) · Nature · doi:10.1038/nature02026 · Cited by 4,248 · cited 3×
“As they were identified with a median of 21 peptides it is unlikely that they were expressed at extremely low levels and their abundance was instead likely misclassified in the genome tagging studies (7, 8).”
BackgroundMethodGlobal analysis of protein expression in yeast
Ghaemmaghami, S., Huh, W.-K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., & Weissman, J. S. (2003) · Nature · doi:10.1038/nature02046 · Cited by 3,750
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
de Godoy, L. M. F., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Fröhlich, F., Walther, T. C., & Mann, M. (2008) · Nature · doi:10.1038/nature07341 · Cited by 873
Self-citationFull dynamic range proteome analysis of S. cerevisiae by targeted proteomics
Picotti, P., Bodenmiller, B., Mueller, L. N., Domon, B., & Aebersold, R. (2009) · Cell · doi:10.1016/j.cell.2009.05.051 · Cited by 744
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
Self-citationPrecision proteomics: The case for high resolution and high mass accuracy
Mann, M., & Kelleher, N. L. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800788105 · Cited by 450
Self-citationProteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans
Malmström, J., Beck, M., Schmidt, A., Lange, V., Deutsch, E. W., & Aebersold, R. (2009) · Nature · doi:10.1038/nature08184 · Cited by 421
Cited by
The CRAPome: a contaminant repository for affinity purification–mass spectrometry data
Mellacheruvu, D., Wright, Z., Couzens, A. L., Lambert, J.-P., St-Denis, N. A., Li, T., Miteva, Y. V., Hauri, S., Sardiu, M. E., Low, T. Y., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2557 · Cited by 1,686
Kulak, N. A., Pichler, G., Paron, I., Nagaraj, N., & Mann, M. (2014) · Nature Methods · doi:10.1038/nmeth.2834 · Cited by 1,719
Self-citationIntegrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma
Gao, Q., Zhu, H., Dong, L., Shi, W., Chen, R., Song, Z., Huang, C., Li, J., Dong, X., Zhou, Y., et al. (2019) · Cell · doi:10.1016/j.cell.2019.08.052 · Cited by 1,096
An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics
Angelidis, I., Simon, L. M., Fernandez, I. E., Strunz, M., Mayr, C. H., Greiffo, F. R., Tsitsiridis, G., Ansari, M., Graf, E., Strom, T.-M., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08831-9 · Cited by 637
Self-citationHebert, A. S., Richards, A. L., Bailey, D. J., Ulbrich, A., Coughlin, E. E., Westphall, M. S., & Coon, J. J. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.034769 · Cited by 528
“Previous single-shot yeast proteome analyses utilized long capillary LC columns (50 cm) and lengthy gradients (240 min) (25, 40, 41) We aimed to achieve comparable or better coverage using a much shorter gradient (70 min).”
Method
Metadata
- Authors
- Thakur, S. S., Geiger, T., Chatterjee, B., Bandilla, P., Fröhlich, F., Cox, J., & Mann, M.
- Venue
- Molecular & Cellular Proteomics
- Publisher
- Elsevier BV
- Published
- 2011-08
- Volume
- 10
- Issue
- 8
- Pages
- M110.003699
- ISSN
- 1535-9476 (ISSN-L)
- OpenAlex
- W2129754968
- Cited by
- 337
- References
- 9
- FWCI
- 19.56
- Type
- journal article
- Language
- en
- Open access
- hybrid
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