ArticleJournal of proteome research2013
Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry.
Article in Journal of proteome research, 2013. 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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Who cites it
13 citing papers in PubMed.
- Structure of cytoplasmic RNA polymerase II.Nature communications · 2026Article
- Characterizing host-microbe interactions with bacterial effector proteins using proximity-dependent biotin identification (BioID).Communications biology · 2025Review
- Recurrent chromosomal translocations in sarcomas create a megacomplex that mislocalizes NuA4/TIP60 to Polycomb target loci.Genes & development · 2022Article
- Interactome Analysis of KIN (Kin17) Shows New Functions of This Protein.Current issues in molecular biology · 2021Article
- Bi-allelic Mutations in EPRS, Encoding the Glutamyl-Prolyl-Aminoacyl-tRNA Synthetase, Cause a Hypomyelinating Leukodystrophy.American journal of human genetics · 2018Article
- Dysregulation of cotranscriptional alternative splicing underlies CHARGE syndrome.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- R2TP/Prefoldin-like component RUVBL1/RUVBL2 directly interacts with ZNHIT2 to regulate assembly of U5 small nuclear ribonucleoprotein.Nature communications · 2017Article
- Absence of neurological abnormalities in mice homozygous for the Polr3a G672E hypomyelinating leukodystrophy mutation.Molecular brain · 2017Article
- Article
- Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology.International journal of molecular sciences · 2016Review
- From raw data to biological discoveries: a computational analysis pipeline for mass spectrometry-based proteomics.Journal of the American Society for Mass Spectrometry · 2015Article
- Recessive mutations in POLR1C cause a leukodystrophy by impairing biogenesis of RNA polymerase III.Nature communications · 2015Article
- PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data.Journal of proteome research · 2014Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Affinity purification combined with tandem mass spectrometry (AP-MS/MS) is a well-established method used to discover interaction partners for a given protein of interest. Because most AP-MS/MS approaches are performed using the soluble fraction of whole cell extracts (WCE), information about the cellular compartments where the interactions occur is lost. More importantly, classical AP-MS/MS often fails to identify interactions that take place in the nonsoluble fraction of the cell, for example, on the chromatin or membranes; consequently, protein complexes that are less soluble are underrepresented. In this paper, we introduce a method called multiple cell compartment AP-MS/MS (MCC-AP-MS/MS), which identifies the interactions of a protein independently in three fractions of the cell: the cytoplasm, the nucleoplasm, and the chromatin. We show that this fractionation improves the sensitivity of the method when compared to the classical affinity purification procedure using soluble WCE while keeping a very high specificity. Using three proteins known to localize in various cell compartments as baits, the CDK9 subunit of transcription elongation factor P-TEFb, the RNA polymerase II (RNAP II)-associated protein 4 (RPAP4), and the largest subunit of RNAP II, POLR2A, we show that MCC-AP-MS/MS reproducibly yields fraction-specific interactions. Finally, we demonstrate that this improvement in sensitivity leads to the discovery of novel interactions of RNAP II carboxyl-terminal domain (CTD) interacting domain (CID) proteins with POLR2A.
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