ArticleBiochimica et biophysica acta. Bioenergetics2021
Quantitative density gradient analysis by mass spectrometry (qDGMS) and complexome profiling analysis (ComPrAn) R package for the study of macromolecular complexes.
Article in Biochimica et biophysica acta. Bioenergetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 28 citations in OpenAlex.
- Mass spectrometry proteomics for studying mitostasis.Protein science : a publication of the Protein Society · 2026Review
- Analysis of Complexome Profiles with the Gaussian Interaction Profiler (GIP) Reveals Novel Protein Complexes inJournal of proteome research · 2024Article
- TLR-mediated aggresome-like induced structures comprise antimicrobial peptides and attenuate intracellular bacterial survival.Molecular biology of the cell · 2024Article
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- The catalytic activity of methyltransferase METTL15 is dispensable for its role in mitochondrial ribosome biogenesis.RNA biology · 2024Article
- Let's make it clear: systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling.Nucleic acids research · 2023Article
- Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution.PLoS computational biology · 2023Article
- Protein Interactome Profiling of Stable Molecular Complexes in Biomaterial Lysate.International journal of molecular sciences · 2022Review
- Complexome Profiling: Assembly and Remodeling of Protein Complexes.International journal of molecular sciences · 2021Review
- YbeY is required for ribosome small subunit assembly and tRNA processing in human mitochondria.Nucleic acids research · 2021Article
- The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches.Frontiers in molecular biosciences · 2021Review
- Complexome Profiling-Exploring Mitochondrial Protein Complexes in Health and Disease.Frontiers in cell and developmental biology · 2021Review
- Mass Spectrometry-Based Proteomics Technologies to Define Endogenous Protein-Protein Interactions and Their Applications to Cancer and Viral Infectious Diseases.Mass spectrometry reviewsReview
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9 authors at 2 institutions in 1 country.
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Abstract
Many cellular processes involve the participation of large macromolecular assemblies. Understanding their function requires methods allowing to study their dynamic and mechanistic properties. Here we present a method for quantitative analysis of native protein or ribonucleoprotein complexes by mass spectrometry following their separation by density - qDGMS. Mass spectrometric quantitation is enabled through stable isotope labelling with amino acids in cell culture (SILAC). We provide a complete guide, from experimental design to preparation of publication-ready figures, using a purposely-developed R package - ComPrAn. As specific examples, we present the use of sucrose density gradients to inspect the assembly and dynamics of the human mitochondrial ribosome (mitoribosome), its interacting proteins, the small subunit of the cytoplasmic ribosome, cytoplasmic aminoacyl-tRNA synthetase complex and the mitochondrial PDH complex. ComPrAn provides tools for analysis of peptide-level data as well as normalization and clustering tools for protein-level data, dedicated visualization functions and graphical user interface. Although, it has been developed for the analysis of qDGMS samples, it can also be used for other proteomics experiments that involve 2-state labelled samples separated into fractions. We show that qDGMS and ComPrAn can be used to study macromolecular complexes in their native state, accounting for the dynamics inherent to biological systems and benefiting from its proteome-wide quantitative and qualitative capability.
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