An integrated workflow for quantitative analysis of the newly synthesized proteome

• Published in: Nature communications Vol. 14; no. 1; pp. 8237 - 16
• Main Authors: Borteçen, Toman, Müller, Torsten, Krijgsveld, Jeroen
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 12-12-2023; Nature Publishing Group; Nature Portfolio
• Subjects: 631/45/475; 631/553/2710; 82/58; Amino acids; Amino Acids - chemistry; Automation; Cell Line; Data analysis; Humanities and Social Sciences; Isotope Labeling - methods; Mass spectrometry; Mass spectroscopy; multidisciplinary; Perturbation; Proteins; Proteome - metabolism; Proteomes; Proteomics; Proteomics - methods; Quantitative analysis; Sample preparation; Science; Science (multidisciplinary); Synthesis; Workflow; γ-Interferon
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-43919-3

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.
Analysis of newly synthesized proteins upon perturbation can provide detailed insights into immediate proteome remodeling, which drives cellular responses. Here, the authors report an optimized semi-automated workflow for the quantitative analysis of the newly synthesized proteome.