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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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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Accounting for population variation in targeted proteomics.

Grant M Fujimoto1, Matthew E Monroe, Larissa Rodriguez

  • 1Biological Sciences Division, Pacific Northwest National Laboratory , 902 Battelle Boulevard, Richland, Washington 99532, United States.

Journal of Proteome Research
|December 11, 2013
PubMed
Summary

Individual human proteomes vary significantly, impacting protein quantification in targeted proteomics. A new Skyline plugin helps researchers identify variable peptides by accessing dbSNP polymorphism data.

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Genetics

Background:

  • Individual proteomes exhibit substantial variation (approx. 10,000 single amino acid variants) compared to the reference human proteome.
  • Population-scale protein sequence diversity can complicate accurate quantification in targeted proteomics experiments.

Purpose of the Study:

  • To develop a tool that aids researchers in identifying peptides with high variability across the human population.
  • To facilitate the consideration of genetic variation in targeted proteomics studies.

Main Methods:

  • Creation of the Population Variation plug-in for Skyline software.
  • Integration of dbSNP polymorphism data for access within the plug-in.
  • Reporting of minor allele frequencies for common polymorphisms associated with user-selected peptides.

Main Results:

  • The Population Variation plug-in provides researchers with a method to assess peptide variability.
  • Demonstration of the tool's utility by applying it to public datasets.
  • Highlighting the significance of accounting for genetic variation in proteomics.

Conclusions:

  • The Population Variation plug-in is a valuable resource for targeted proteomics researchers.
  • Considering population-specific genetic variation is crucial for accurate protein quantification.
  • The tool enhances the reliability of targeted proteomics by enabling informed peptide selection.