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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Protein Networks02:26

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Updated: Aug 23, 2025

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
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Exploring Protein Interactome Data with IPinquiry: Statistical Analysis and Data Visualization by Spectral Counts.

Lauriane Kuhn1, Timothée Vincent2, Philippe Hammann1

  • 1Plateforme protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France.

Methods in Molecular Biology (Clifton, N.J.)
|October 29, 2022
PubMed
Summary

We developed IPinquiry, an R package for immunoprecipitation mass spectrometry (IP-MS) analysis. It simplifies protein-protein interaction network exploration for biologists using spectral count quantification.

Keywords:
Data processingDifferential analysisImmunoprecipitationMass spectrometryR packageSpectral countsVolcano plots

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Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation
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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Systems Biology

Background:

  • Immunoprecipitation mass spectrometry (IP-MS) is crucial for identifying protein-protein interactions and mapping complex protein networks.
  • Existing IP-MS analysis workflows can be complex, posing challenges for biologists seeking to explore protein interactomes.
  • A need exists for streamlined computational tools to facilitate the analysis and interpretation of IP-MS data.

Purpose of the Study:

  • To introduce IPinquiry, a novel R package designed for the analysis of immunoprecipitation mass spectrometry (IP-MS) data.
  • To provide a user-friendly R pipeline for biologists to explore protein-protein interaction networks derived from IP-MS experiments.
  • To enable differential analysis, annotation retrieval, result export, and visualization of IP-MS data.

Main Methods:

  • Development of the IPinquiry R package utilizing spectral count quantification for IP-MS data.
  • Implementation of a simplified pipeline for data loading, processing, and analysis.
  • Integration of functions for differential protein accumulation analysis between experimental groups.
  • Inclusion of modules for protein annotation retrieval, results export, and graphical representation.

Main Results:

  • IPinquiry offers a straightforward R-based pipeline for IP-MS data analysis, reducing the number of processing steps.
  • The package facilitates differential analysis of protein abundance between different IP experiment groups.
  • IPinquiry supports the retrieval of protein annotations and generates various plots for data visualization and exploration.
  • A step-by-step procedure for interactome analysis using IPinquiry is described, from data input to output.

Conclusions:

  • IPinquiry provides a valuable and accessible tool for biologists to perform IP-MS interactome analysis.
  • The package simplifies complex data exploration, enabling efficient identification of protein-protein interactions.
  • IPinquiry enhances the utility of IP-MS by offering integrated analysis, annotation, and visualization capabilities within a single R environment.