An integrated workflow for quantitative analysis of the newly synthesized proteome
Open accessPublished version of a preprint
Abstract
The analysis of proteins that are newly synthesized upon a cellular perturbation can provide detailed insight into the proteomic response that is elicited by specific cues. This can be investigated by pulse-labeling of cells with clickable and stable-isotope-coded amino acids for the enrichment and mass spectrometric characterization of newly synthesized proteins (NSPs), however convoluted protocols prohibit their routine application. Here we report the optimization of multiple steps in sample preparation, mass spectrometry and data analysis, and we integrate them into a semi-automated workflow for the quantitative analysis of the newly synthesized proteome (QuaNPA). Reduced input requirements and data-independent acquisition (DIA) enable the analysis of triple-SILAC-labeled NSP samples, with enhanced throughput while featuring high quantitative accuracy. We apply QuaNPA to investigate the time-resolved cellular response to interferon-gamma (IFNg), observing rapid induction of targets 2 h after IFNg treatment. QuaNPA provides a powerful approach for large-scale investigation of NSPs to gain insight into complex cellular processes.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
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 · see citing works
mRNAs, proteins and the emerging principles of gene expression control
Buccitelli, C., & Selbach, M. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0258-4 · Cited by 1,243 · see citing works
Frankenfield, A. M., Ni, J., Ahmed, M., & Hao, L. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00145 · Cited by 321 · see citing works
Selective enrichment of newly synthesized proteins for quantitative secretome analysis
Eichelbaum, K., Winter, M., Diaz, M. B., Herzig, S., & Krijgsveld, J. (2012) · Nature Biotechnology · doi:10.1038/nbt.2356 · Cited by 248 · see citing works
Self-citationTranslational Control in the Brain in Health and Disease
Sossin, W. S., & Costa-Mattioli, M. (2019) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a032912 · Cited by 138 · see citing works
Flagged first, then by citations
- Authors
- Borteçen, T., Müller, T., & Krijgsveld, J.
- Affiliations
- German Cancer Research Center (DE)
- Heidelberg University (DE)
- Corresponding author
- Krijgsveld, Jeroen
- Venue
- Nature Communications
- Published
- 2023-12-12
- Volume
- 14
- Issue
- 1
- Pages
- 8237-8237
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC10716174
- OpenAlex
- W4389614649
- Cited by
- 19
- References
- 5
- Citations by year
- 2026: 1 · 2025: 9 · 2024: 7 · 2023: 2
- FWCI
- 1.74
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Bundesministerium für Bildung und Forschung (161L0212A)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- newly synthesized proteins, pulse labeling, stable isotope labeling, data-independent acquisition, semi-automated workflow, interferon-gamma response, time-resolved proteomics, sample preparation optimization
- MeSH terms
- Amino Acids, Cell Line, Isotope Labeling, Proteome, Proteomics, Workflow
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
