Toward a hypothesis‐free understanding of how phosphorylation dynamically impacts protein turnover. Issue 3 (7th December 2022)

• Record Type: Journal Article
• Authors: Li, Wenxue; Salovska, Barbora; Fornasiero, Eugenio F.; Liu, Yansheng
• Other Names: Liu Yansheng guestEditor.; Salovska Barbora guestEditor.
• Is Part Of: Proteomics. Volume 23:Issue 3/4(2023)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2022-12-07
• Subjects: clustering -- data analysis -- DeltaSILAC -- DIA‐MS -- peptidoform -- phosphorylation -- protein turnover -- pulse SILAC -- time course; Proteins -- Separation -- Periodicals; Bioinformatics -- Periodicals; Proteomics -- Periodicals; Genomes -- Periodicals; Molecular genetics -- Periodicals; 572.605
• DOI: 10.1002/pmic.202100387
• Languages: English
• ISSNs: 1615-9853

Abstract

Abstract: The turnover measurement of proteins and proteoforms has been largely facilitated by workflows coupling metabolic labeling with mass spectrometry (MS), including dynamic stable isotope labeling by amino acids in cell culture (dynamic SILAC) or pulsed SILAC (pSILAC). Very recent studies including ours have integrated themeasurement of post‐translational modifications (PTMs) at the proteome level (i.e., phosphoproteomics) with pSILAC experiments in steady state systems, exploring the link between PTMs and turnover at the proteome‐scale. An open question in the field is how to exactly interpret these complex datasets in a biological perspective. Here, we present a novel pSILAC phosphoproteomic dataset which was obtained during a dynamic process of cell starvation using data‐independent acquisition MS (DIA‐MS). To provide an unbiased "hypothesis‐free" analysis framework, we developed a strategy to interrogate how phosphorylation dynamically impacts protein turnover across the time series data. With this strategy, we discovered a complex relationship between phosphorylation and protein turnover that was previously underexplored. Our results further revealed a link between phosphorylation stoichiometry with the turnover of phosphorylated peptidoforms. Moreover, our results suggested that phosphoproteomic turnover diversity cannot directly explain the abundance regulation of phosphorylation during cell starvation, underscoring the importance of future studies addressing PTM site‐resolved protein turnover.