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Selective enrichment of newly synthesized proteins for quantitative secretome analysis
Abstract
Secreted proteins constitute a large and biologically important subset of proteins that are involved in cellular communication, adhesion and migration. Yet secretomes are understudied because of technical limitations in the detection of low-abundance proteins against a background of serum-containing media. Here we introduce a method that combines click chemistry and pulsed stable isotope labeling with amino acids in cell culture to selectively enrich and quantify secreted proteins. The combination of these two labeling approaches allows cells to be studied irrespective of the complexity of the background proteins. We provide an in-depth and differential secretome analysis of various cell lines and primary cells, quantifying secreted factors, including cytokines, chemokines and growth factors. In addition, we reveal that serum starvation has a marked effect on secretome composition. We also analyze the kinetics of protein secretion by macrophages in response to lipopolysaccharides.
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“the increase in the calculated ‘degradation rate’ – likely reflecting depletion by secretion, or “decreased cellular half life” – of proteins from the recently-characterized secretome of LPS stimulated mouse macrophages (33) (P < 10−10, LPS vs. MOCK; Wilcoxon rank-sum Test, fig. S9C).”
From Dynamic profiling of the protein life cycle in response to pathogens (2015) · cites this paper as [33]
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“Although some of this is due to turnover from increased secretion of some proteins (figs. S9C, S18), excluding the secretome (33) from our analysis did not strongly alter this global trend (fig. S18).”
From Dynamic profiling of the protein life cycle in response to pathogens (2015) · cites this paper as [33]
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Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890
Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855
Bioconductor: open software development for computational biology and bioinformatics
Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. (2004) · Genome biology · doi:10.1186/gb-2004-5-10-r80 · Cited by 12,082
Smyth, G. K. (2004) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1027 · Cited by 11,829
SignalP 4.0: discriminating signal peptides from transmembrane regions
Petersen, T. N., Brunak, S., von Heijne, G., & Nielsen, H. (2011) · Nature Methods · doi:10.1038/nmeth.1701 · Cited by 8,847
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
Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment
Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., & Mann, M. (2011) · Journal of Proteome Research · doi:10.1021/pr101065j · Cited by 5,520
Anderson, N. L., & Anderson, N. G. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r200007-mcp200 · Cited by 4,414
Widespread changes in protein synthesis induced by microRNAs
Selbach, M., Schwanhäusser, B., Thierfelder, N., Fang, Z., Khanin, R., & Rajewsky, N. (2008) · Nature · doi:10.1038/nature07228 · Cited by 3,429
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Baeza, J., Coons, B. E., Lin, Z., Riley, J. S., Mendoza, M. R., Peranteau, W. H., & Garcia, B. A. (2024) · Cell Reports Methods · doi:10.1016/j.crmeth.2024.100713 · Cited by 2
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Holloway, R. K., Zhang, L., Molina-González, I., Ton, K., Nicoll, J. A. R., Boardman, J. P., Liang, Y., Williams, A., & Miron, V. E. (2024) · Figshare · doi:10.6084/m9.figshare.26577053
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Metadata
- Authors
- Eichelbaum, K., Winter, M., Diaz, M. B., Herzig, S., & Krijgsveld, J.
- Affiliations
- European Molecular Biology Laboratory (DE)
- German Cancer Research Center (DE)
- Corresponding author
- Krijgsveld, Jeroen
- Venue
- Nature Biotechnology
- Published
- 2012-09-23
- Volume
- 30
- Issue
- 10
- Pages
- 984-990
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2031704362
- Cited by
- 248
- References
- 44
- Citations by year
- 2026: 9 · 2025: 8 · 2024: 13 · 2023: 18 · 2022: 21 · 2021: 20 · 2020: 31 · 2019: 17 · 2018: 21 · 2017: 20 · 2016: 21 · 2015: 13 · 2014: 14 · 2013: 20 · 2012: 2
- FWCI
- 6.91
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Site cant be reached (submittedVersion)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Organic Chemistry › Click Chemistry and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced Biosensing Techniques and Applications
- Keywords
- secretome, secreted proteins, protein enrichment, click chemistry, quantitative proteomics, low-abundance proteins, cytokines, chemokines, growth factors, serum deprivation, macrophages, lipopolysaccharide response
- MeSH terms
- Cell Line, Culture Media, Humans, Isotope Labeling, Kinetics, Lipopolysaccharides, Macrophage Activation, Proteins, Protein Biosynthesis, Culture Media, Serum-Free, Hepatocytes, Click Chemistry, Protein Interaction Maps
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