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 calculated degradation rate of proteins from the secretome of LPS-stimulated mouse macrophages increases (P < 10−10, LPS vs MOCK).
“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]
Removing the secretome from the analysis did not substantially change the global pattern of equal roles for degradation and translation.
“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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- 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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