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Related Concept Videos

Proteomics01:33

Proteomics

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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...
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Peptide Identification Using Tandem Mass Spectrometry01:33

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Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
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Immunoprecipitation01:20

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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.
Chromatin Immunoprecipitation
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Protein Networks02:26

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Enzyme-Linked Immunosorbent Assay01:33

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In 1971, Peter Perlman and Eva Engvall developed an Enzyme-linked immunosorbent assay (ELISA or EIA). ELISA differs from western blot in that the assays are conducted in microtiter plates or in vivo rather than on an absorbent membrane.
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The Proteasome Structure

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The ubiquitin-proteasome pathway is a well-known mechanism utilized by eukaryotic cells to remove cytoplasmic proteins that are misfolded, damaged, or no longer needed. In this pathway, the protein that needs to be eliminated undergoes a process called ubiquitination, where a chain of ubiquitin molecules is attached to the 48th lysine residue of the target protein. This ubiquitin modification helps the proteasome distinguish between a target protein and a healthy protein.
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Related Experiment Video

Updated: Jun 24, 2025

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis
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Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis

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The Immunopeptidomics Ontology (ImPO).

Daniel Faria1, Patrícia Eugénio2, Marta Contreiras Silva2

  • 1INESC-ID, Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol, 9, Lisboa 1000-029, Portugal.

Database : the Journal of Biological Databases and Curation
|June 10, 2024
PubMed
Summary

The ImmunoPeptidomics Ontology (ImPO) standardizes terminology for immunopeptidomics data. This ontology facilitates data integration and bridges the gap between clinical proteomics and genomics for cancer research.

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Related Experiment Videos

Last Updated: Jun 24, 2025

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis
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Peptide and Protein Quantification Using Automated Immuno-MALDI iMALDI
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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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Area of Science:

  • Immunology and Bioinformatics
  • Computational Biology and Systems Biology

Background:

  • Adaptive immunity relies on Major Histocompatibility Complex Class I (MHC-I) presenting peptides for cell recognition.
  • Immunopeptidomics studies the diverse peptides presented by cells, crucial for understanding cancer immunotherapies.
  • The emerging field of immunopeptidomics lacks standardized terminology and semantics, hindering data integration and clinical application.

Purpose of the Study:

  • To develop the first standardized terminology and semantic framework for the immunopeptidomics domain.
  • To create the ImmunoPeptidomics Ontology (ImPO) to encapsulate and systematize immunopeptidomics data.
  • To bridge the gap between proteomics and genomics communities in cancer research.

Main Methods:

  • Development of the ImmunoPeptidomics Ontology (ImPO) using expert knowledge.
  • Systematization of data from immunopeptidomics experiments and bioinformatics analyses.
  • Integration of ImPO with 24 existing ontologies, including NCI Thesaurus and Mondo Disease Ontology.

Main Results:

  • ImPO provides a standardized vocabulary and semantic structure for immunopeptidomics data.
  • The ontology facilitates data integration, querying, inference, and knowledge generation.
  • ImPO establishes cross-references to relevant biomedical ontologies, enhancing data interoperability.

Conclusions:

  • ImPO is the first ontology to standardize immunopeptidomics terminology and semantics.
  • This standardization is essential for managing complex and heterogeneous immunopeptidomics data.
  • ImPO supports data integration and knowledge discovery, crucial for advancing cancer immunogenomics and clinical applications.