Recent advancements in mass spectrometry-based tools to investigate newly synthesized proteins

Wouter van Bergen, Albert J R Heck, Marc P Baggelaar

Research output: Contribution to journalArticleAcademicpeer-review

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.

Original languageEnglish
Article number102074
JournalCurrent Opinion in Chemical Biology
Volume66
Early online date5 Aug 2021
DOIs
Publication statusPublished - Feb 2022

Keywords

  • Bio-orthogonal noncanonical amino acid tagging (BONCAT)
  • Mass spectrometry
  • Newly synthesized proteins
  • Protein dynamics
  • Protein synthesis
  • Proteomics
  • Puromycin
  • Stable isotope labeling by amino acids in cell culture (SILAC)

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