Recent advancements in mass spectrometry–based tools to investigate newly synthesized proteins. (February 2022)

• Record Type: Journal Article
• Authors: van Bergen, Wouter; Heck, Albert J.R.; Baggelaar, Marc P.
• Is Part Of: Current opinion in chemical biology. Volume 66(2022)
• Publication Date: 2022-02
• Subjects: Newly synthesized proteins -- Protein synthesis -- Protein dynamics -- Mass spectrometry -- Proteomics -- Bio-orthogonal noncanonical amino acid tagging (BONCAT) -- Puromycin -- Stable isotope labeling by amino acids in cell culture (SILAC); AHA L-azidohomoalanine -- ANL L-azidonorleucine -- BONCAT Bio-orthogonal non-canonical amino acid tagging -- HPG L-homopropargylglycine -- iTRAQ Isobaric tag for relative and absolute quantitation -- LC Liquid chromatography -- LPS Lipopolysaccharide -- mePROD Multiplexed enhanced protein dynamics -- MITNCAT Multiplex isobaric tagging/non-canonical amino acid tagging multiplex -- mPDP Multiplexed proteome dynamics profiling -- mRNA Messenger ribonucleic acid -- MS Mass spectrometry -- NCAA Non-canonical amino acid -- NSP Newly synthesized protein -- OPP O-propargyl-puromycin -- pSILAC pulsed SILAC -- PUNCH–P Puromycin-associated nascent chain proteomics -- QuaNCAT Quantitative non-canonical amino acid tagging -- RNA Ribonucleic acid -- SILAC Stable isotope labeling by amino acids in cell culture -- TMT Tandem mass tag -- TNF-α Tumor necrosis factor alpha -- tRNA Transfer-ribonucleic acid; Bioorganic chemistry -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Clinical biochemistry -- Periodicals; Biochemistry -- Periodicals; Chimie bio-organique -- Périodiques; Biologie -- Périodiques; 572.05
• DOI: 10.1016/j.cbpa.2021.07.001
• Languages: English
• ISSNs: 1367-5931

Abstract

Abstract: Tight regulation of protein translation drives the proteome to undergo changes under influence of extracellular or intracellular signals. Despite mass spectrometry–based proteomics being an excellent method to study differences in protein abundance in complex proteomes, analyzing minute or rapid changes in protein synthesis and abundance remains challenging. Therefore, several dedicated techniques to directly detect and quantify newly synthesized proteins have been developed, notably puromycin-based, bio-orthogonal noncanonical amino acid tagging–based, and stable isotope labeling by amino acids in cell culture–based methods, combined with mass spectrometry. These techniques have enabled the investigation of perturbations, stress, or stimuli on protein synthesis. Improvements of these methods are still necessary to overcome various remaining limitations. Recent improvements include enhanced enrichment approaches and combinations with various stable isotope labeling techniques, which allow for more accurate analysis and comparison between conditions on shorter timeframes and in more challenging systems. Here, we aim to review the current state in this field. Graphical abstract: Image 1