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Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Related Experiment Video

Updated: Jun 15, 2026

Biochemical Purification and Proteomic Characterization of Amyloid Fibril Cores from the Brain

Biochemical Purification and Proteomic Characterization of Amyloid Fibril Cores from the Brain

Published on: April 28, 2022

CPFP: a central proteomics facilities pipeline.

David C Trudgian¹, Benjamin Thomas, Simon J McGowan

¹Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK. dctrud@ccmp.ox.ac.uk

Bioinformatics (Oxford, England)

|March 2, 2010

Summary

This summary is machine-generated.

The Central Proteomics Facilities Pipeline (CPFP) streamlines peptide and protein analysis from LC-MS/MS data for core facilities. This tool simplifies data handling for clients and reduces staff workload through automated identification and validation.

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Last Updated: Jun 15, 2026

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Published on: April 28, 2022

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Published on: October 20, 2016

Area of Science:

Proteomics
Biotechnology
Bioinformatics

Background:

The Central Proteomics Facilities Pipeline (CPFP) is a novel software solution designed for proteomics core facilities.
It addresses the need for efficient and accessible analysis of LC-MS/MS datasets.

Purpose of the Study:

To introduce the CPFP as a user-friendly web interface for peptide and protein identification, validation, and quantitation.
To reduce the data analysis burden on proteomics core facility staff.
To empower facility clients with easy access and control over their experimental data.

Main Methods:

Utilizes multiple search engines for peptide identification.
Combines and validates outputs from various search engines using advanced techniques.
Employs cluster execution for scalable job processing to meet growing demand.

Main Results:

Provides a streamlined pipeline for LC-MS/MS data analysis.
Enhances the accuracy and reliability of peptide and protein identification through multi-engine validation.
Offers a scalable solution for proteomics data processing.

Conclusions:

The CPFP is the first analysis pipeline specifically tailored for proteomics core facilities.
It significantly improves efficiency in data analysis and accessibility for facility users.
The pipeline's design supports scalability to accommodate increasing analytical demands.