Cover Image

An integrated workflow for quantitative analysis of the newly synthesized proteome

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...

Full description

Saved in:
Bibliographic Details
Main Authors: Bortecen, Toman (Author) , Müller, Torsten (Author) , Krijgsveld, Jeroen (Author)
Format: Article (Journal)
Language:English
Published: 12 December 2023
In: Nature Communications
Year: 2023, Volume: 14, Pages: 1-16
ISSN:2041-1723
DOI:10.1038/s41467-023-43919-3
Online Access:Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1038/s41467-023-43919-3
Verlag, lizenzpflichtig, Volltext: https://www.nature.com/articles/s41467-023-43919-3
Get full text
Author Notes:Toman Borteçen, Torsten Müller & Jeroen Krijgsveld
Description
Summary: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.
Item Description:Gesehen am 26.02.2024
Physical Description:Online Resource
ISSN:2041-1723
DOI:10.1038/s41467-023-43919-3

Similar Items