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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...

Protein Complex Assembly

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

Protein Complex Assembly

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

Protein Networks

Protein Networks

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.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

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Related Experiment Video

Updated: May 15, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

CAPER: a chromosome-assembled human proteome browsER.

Feifei Guo¹, Dan Wang, Zhongyang Liu

¹Institute of Basic Medical Sciences and School of Basic Medicine, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100005, China.

Journal of Proteome Research

|December 22, 2012

Summary

This summary is machine-generated.

We developed CAPER, a user-friendly web tool for visualizing human proteomic data. This Chromosome-Assembled human Proteome browsER (CAPER) aids in organizing and analyzing large datasets for genome research.

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Introductory Analysis and Validation of CUT&RUN Sequencing Data

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

Area of Science:

Proteomics
Bioinformatics
Genomics

Background:

High-throughput proteomic experiments generate vast datasets.
Effective integration and analysis of proteomic data are crucial for understanding the human genome.
Chromosome-based visualization offers a powerful approach for organizing complex biological information.

Purpose of the Study:

To develop a user-friendly, web-based tool for visualizing and analyzing human proteomic data.
To facilitate the integration and interpretation of proteomic, transcriptomic, and genomic information.
To support the Chromosome-Centric Human Proteome Project and research in human physiology and pathology.

Main Methods:

Development of a web-based platform named Chromosome-Assembled human Proteome browsER (CAPER).
Implementation of two distinct visualization strategies: track-view for sequence/site data and heatmap-view for functional annotations.
Integration of Google Map-like navigation for multi-scale data browsing and exploration.

Main Results:

CAPER provides comprehensive visualization of proteomic datasets and annotations.
The tool enables seamless switching between track-view and heatmap-view for enhanced data interpretation.
Smooth navigation and zooming capabilities allow for detailed examination of data at chromosome level.

Conclusions:

CAPER significantly facilitates the annotation and functional interpretation of the human genome using proteomic data.
The tool enhances the integration of multi-omics data, aiding in physiological and pathological research.
CAPER serves as a valuable resource for the Chromosome-Centric Human Proteome Project.