ArticleNature communications2023
An integrated workflow for quantitative analysis of the newly synthesized proteome.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 20 citations in OpenAlex.
- Exercise-induced protein lactylation: From molecular mechanisms to precision health applications.iScience · 2026Review
- A step-by-step guide to performing cancer metabolism research using custom-made media.Life science alliance · 2026Article
- Principles of protein abundance regulation across single cells in a mammalian tissue.bioRxiv : the preprint server for biology · 2025Article
- A robust multiplex-DIA workflow profiles protein turnover regulations associated with cisplatin resistance and aneuploidy.Nature communications · 2025Article
- mTORC1 cooperates with tRNA wobble modification to sustain the protein synthesis machinery.Nature communications · 2025Article
- Impact of protein degradation and cell growth on mammalian proteomes.bioRxiv : the preprint server for biology · 2025Article
- Combining Data Independent Acquisition With Spike-In SILAC (DIA-SiS) Improves Proteome Coverage and Quantification.Molecular & cellular proteomics : MCP · 2024Article
- Proteomics applications in next generation induced pluripotent stem cell models.Expert review of proteomics · 2024Review
- Improved detection and consistency of RNA-interacting proteomes using DIA SILAC.Nucleic acids research · 2024Article
- An integrated workflow for quantitative analysis of the newly synthesized proteome.Nature communications · 2023Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.