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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

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Published on: October 19, 2021

Network-based inference from complex proteomic mixtures using SNIPE.

David P Nusinow¹, Adam Kiezun, Daniel J O'Connell

¹Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA.

Bioinformatics (Oxford, England)

|October 13, 2012

Summary

This summary is machine-generated.

This study introduces SNIPE (Software for Network Inference of Proteomics Experiments), a tool that enhances shotgun proteomics by detecting low-abundance proteins like transcription factors. SNIPE improves the analysis of complex biological samples, aiding in the discovery of previously undetectable proteins.

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Area of Science:

Proteomics
Systems Biology
Bioinformatics

Background:

Shotgun proteomics struggles to detect low-abundance proteins, such as transcription factors, in complex biological samples.
Assaying these proteins within the context of the entire proteome is crucial for experimental biology.

Purpose of the Study:

To develop a method for detecting low-abundance proteins that are otherwise undetectable in shotgun proteomic data.
To enhance the utility of proteomics experiments for studying transcription factors and other critical regulatory proteins.

Main Methods:

Network-based inference approach named SNIPE (Software for Network Inference of Proteomics Experiments).
Integration of spectral counts from paired case-control samples within a network neighborhood.
Statistical assessment of enrichment likelihood using a permutation test.

Main Results:

SNIPE successfully highlights likely active but undetectable proteins in shotgun proteomic samples.
Application in murine tooth development identified several key proteins, including previously unreported transcription factors.
Experimental evidence confirmed SNIPE's ability to uncover critical low-abundance proteins.

Conclusions:

SNIPE significantly enhances the utility of shotgun proteomics data.
The method facilitates the study of poorly detected proteins in complex biological mixtures.
SNIPE aids in the discovery of novel transcription factors and improves proteomic analysis.