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Immunoprecipitation, or IP, is a widely used technique that employs protein-antibody interactions to isolate proteins or protein complexes in their native state for studying protein-protein interactions, quaternary structures, or supramolecular complexes. Various modifications of the technique, including chromatin IP, cross-linking IP, and fluorescence IP, are commonly used.
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Related Experiment Video

Updated: Jun 20, 2025

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Published on: November 17, 2019

IMmuneCite: an integrated workflow for analysis of immune enriched spatial proteomic data.

Arianna Barbetta¹, Sarah Bangerth¹, Jason T C Lee¹

¹University of Southern California.

Research Square

|July 23, 2024

Summary

This summary is machine-generated.

IMmuneCite is a new computational tool that accurately identifies 32 immune cell phenotypes in spatial proteomics data. This framework enhances immune microenvironment analysis across species and applications.

Keywords:

Immune Microenvironment Informatics Pipeline Single Cell Proteomics Spatial Biology

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Last Updated: Jun 20, 2025

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

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Published on: November 17, 2019

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Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

Area of Science:

Immunology
Computational Biology
Proteomics

Background:

Spatial proteomics offers single-cell resolution for tissue analysis.
Accurate cell segmentation and phenotyping remain challenging.
Complex immune landscapes require sophisticated computational tools.

Purpose of the Study:

Introduce IMmuneCite, a computational framework for spatial proteomics.
Improve the creation of single-cell datasets for immune cell analysis.
Enable high-fidelity investigation of the immune microenvironment.

Main Methods:

Developed IMmuneCite for comprehensive image pre-processing.
Applied the framework to human and murine liver tissue spatial proteomics data.
Focused on defining discrete immune cell phenotypes and reducing nonbiological clusters.

Main Results:

Identified 32 discrete immune cell phenotypes in human liver samples.
Reduced nonbiological cell clusters caused by marker co-localization.
Demonstrated versatility across species and antibody panels.
Enabled deep characterization of immune cell functional states.

Conclusions:

IMmuneCite is a user-friendly, integrated computational platform.
Facilitates cross-species investigation of the immune microenvironment.
Ensures creation of focused, spatially resolved single-cell proteomic datasets for high-fidelity analysis.