The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
Proteome, Phosphoproteome, and N-Glycoproteome Are Quantitatively Preserved in Formalin-Fixed Paraffin-Embedded Tissue and Analyzable by High-Resolution Mass Spectrometry
Open accessAbstract
Tissue samples in biobanks are typically formalin-fixed and paraffin-embedded (FFPE), in which form they are preserved for decades. It has only recently been shown that proteins in FFPE tissues can be identified by mass spectrometry-based proteomics but analysis of post-translational modifications is thought to be difficult or impossible. The filter aided sample preparation (FASP) method can analyze proteomic samples solubilized in high concentrations of SDS and we use this feature to develop a simple protocol for FFPE analysis. Combination with simple pipet-tip based peptide fractionation identified about 5000 mouse liver proteins in 24 h measurement time-the same as in fresh tissue. Results from the FFPE-FASP procedure do not indicate any discernible changes due to storage time, hematoxylin staining or laser capture microdissection. We compared fresh against FFPE tissue using the SILAC mouse and found no significant qualitative or quantitative differences between these samples either at the protein or the peptide level. Application of our FFPE-FASP protocol to phosphorylation and N-glycosylation pinpointed nearly 5000 phosphosites and 1500 N-glycosylation sites. Analysis of FFPE tissue of the SILAC mouse revealed that these post-translational modifications were quantitatively preserved. Thus, FFPE biobank material can be analyzed by quantitative proteomics at the level of proteins and post-translational modifications.
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Cites
Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855
Self-citationUniversal sample preparation method for proteome analysis
Wiśniewski, J. R., Zougman, A., Nagaraj, N., & Mann, M. (2009) · Nature Methods · doi:10.1038/nmeth.1322 · Cited by 8,352
Self-citationMass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955
Self-citationOng, S.-E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., & Mann, M. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m200025-mcp200 · Cited by 5,574
Self-citationMass spectrometry–based proteomics turns quantitative
Ong, S.-E., & Mann, M. (2005) · Nature Chemical Biology · doi:10.1038/nchembio736 · Cited by 1,572
Self-citationFunctional and quantitative proteomics using SILAC
Mann, M. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2067 · Cited by 931
Self-citationKrüger, M., Moser, M., Ussar, S., Thievessen, I., Luber, C. A., Forner, F., Schmidt, S., Zanivan, S., Fässler, R., & Mann, M. (2008) · Cell · doi:10.1016/j.cell.2008.05.033 · Cited by 680
Self-citationPan, C., Kumar, C., Bohl, S., Klingmueller, U., & Mann, M. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800258-mcp200 · Cited by 561
Self-citationWiśniewski, J. R., Zougman, A., & Mann, M. (2009) · Journal of Proteome Research · doi:10.1021/pr900748n · Cited by 545
Self-citationA 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
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Self-citationProteomic maps of breast cancer subtypes
Tyanova, S., Albrechtsen, R., Kronqvist, P., Cox, J., Mann, M., & Geiger, T. (2016) · Nature Communications · doi:10.1038/ncomms10259 · Cited by 328
Self-citationInflammatory signaling in human tuberculosis granulomas is spatially organized
Marakalala, M. J., Raju, R. M., Sharma, K., Zhang, Y. J., Eugenin, E. A., Prideaux, B., Daudelin, I. B., Chen, P.-Y., Booty, M. G., Kim, J. H., et al. (2016) · Nature Medicine · doi:10.1038/nm.4073 · Cited by 308
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Metadata
- Authors
- Ostasiewicz, P., Zielinska, D. F., Mann, M., & Wiśniewski, J. R.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2010-05-26
- Volume
- 9
- Issue
- 7
- Pages
- 3688-3700
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- OpenAlex
- W2012914501
- Cited by
- 234
- References
- 11
- FWCI
- 9.53
- Type
- journal article
- Language
- en
- Open access
- green
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- Ostasiewicz, P., Zielinska, D. F., Mann, M., & Wiśniewski, J. R. (2010). Proteome, Phosphoproteome, and N-Glycoproteome Are Quantitatively Preserved in Formalin-Fixed Paraffin-Embedded Tissue and Analyzable by High-Resolution Mass Spectrometry. Journal of Proteome Research. https://doi.org/10.1021/pr100234w
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