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Related Concept Videos

Proteomics01:33

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...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Protein Networks02:26

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: Jul 17, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

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Annotating the human proteome: beyond establishing a parts list.

Michael Mueller1, Lennart Martens, Rolf Apweiler

  • 1EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.

Biochimica Et Biophysica Acta
|January 16, 2007
PubMed
Summary

Understanding human gene function requires studying proteins, not just DNA sequences. Proteomics offers advanced tools to analyze protein expression and modifications, crucial for uncovering cellular functions and phenotypes.

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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Area of Science:

  • Genomics and Proteomics
  • Molecular Biology
  • Bioinformatics

Background:

  • The completion of the human genome sequence has shifted research focus towards identifying and characterizing functional genomic elements, particularly genes.
  • Gene prediction algorithms and existing transcript/protein data have identified most human exons, creating a foundational 'parts list' for the genome.
  • Studying gene function at the protein level is essential, as variations in protein isoforms and quantity, which influence phenotype, are often not discernible from sequence or transcript data alone.

Purpose of the Study:

  • To highlight the critical role of proteomics in understanding gene function beyond genomic and transcriptomic levels.
  • To emphasize the need for integrated public domain databases for managing and presenting scattered protein function data.
  • To advocate for the development of resources that move beyond a simple 'parts list' by integrating heterogeneous data.

Main Methods:

  • Leveraging advancements in proteomics technologies for measuring protein expression, post-translational modifications, subcellular localization, and complex assembly.
  • Utilizing existing transcript and protein information alongside improved gene prediction algorithms.
  • Compiling and integrating scattered data from multiple resources on human protein function.

Main Results:

  • Proteomics technologies now enable comprehensive analysis of protein expression, modifications, localization, and interactions.
  • A significant amount of data on human protein function exists but is fragmented across various resources.
  • The need for centralized, accessible, and integrated databases for protein function information is evident.

Conclusions:

  • Protein-level analysis is vital for a complete understanding of cellular functions and phenotypes, complementing genomic and transcriptomic studies.
  • Public domain databases are crucial for consolidating and disseminating scattered protein function data in a usable format.
  • Integrating heterogeneous data into comprehensive resources is key to advancing the study of gene function beyond basic identification.