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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Three-Domain System of Life01:21

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Ribosomal RNA (rRNA) sequence analysis revealed three distinct groups of cells: eukaryotes, bacteria, and archaea. In 1978, Carl R. Woese proposed the concept of domains, a taxonomic level above kingdoms, to differentiate these groups. He suggested that archaea and bacteria, despite their similar appearance, represent separate domains. Domains differ in rRNA, membrane lipid structure, transfer RNA, and antibiotic sensitivity.In this classification, animals, plants, and fungi belong to the...
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Membrane Domains01:18

Membrane Domains

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The membrane domains concentrate specific lipids and proteins at one place within the membrane, which helps in cell signaling, adhesion, and other critical cellular processes. These domains can differ in size, composition, function, and lifespan.
Protein Domains
The membrane comprises a group of distinct proteins responsible for carrying out a cell's specific function. For example, the plasma membrane of the human sperm, or a single germ cell, contains a unique set of proteins in the...
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Three Developmental Domains01:29

Three Developmental Domains

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Human development is typically examined across three main domains: physical, cognitive, and socio-emotional. These domains represent the significant areas of change and continuity throughout the lifespan, from infancy to late adulthood.
Physical Development
Physical processes, also known as maturation, encompass the biological changes that occur across an individual's life. These changes begin with genetic inheritance and continue through various stages, including growth in height and weight,...
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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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Conservation of Protein Domains02:26

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A Quantitative Glycomics and Proteomics Combined Purification Strategy
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Quantitative Proteomics Data in the Public Domain: Challenges and Opportunities.

Andrew F Jarnuczak1, Tobias Ternent1, Juan Antonio Vizcaíno2

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.

Methods in Molecular Biology (Clifton, N.J.)
|April 14, 2019
PubMed
Summary

Quantitative proteomics is now a multidimensional field. Publicly shared data and analysis results, like those in the PRIDE database, offer vast opportunities for new discoveries through data reuse and meta-analysis.

Keywords:
Data (re)analysisData repositoryMass spectrometryPRIDE databaseQuantitative proteomics

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Area of Science:

  • Proteomics
  • Bioinformatics

Background:

  • Mass spectrometry-based proteomics has evolved from a qualitative to a quantitative discipline.
  • Systematic protein expression profiling is now a standard component of many research studies.

Purpose of the Study:

  • To describe public proteomics resources for quantitative data.
  • To guide researchers in reusing and reanalyzing publicly available proteomics data.
  • To highlight potential pitfalls and best practices in quantitative proteomics data reuse.

Main Methods:

  • Review of mainstream public proteomics resources.
  • Discussion of considerations for data reuse and reanalysis.
  • Case studies and experiences in quantitative data utilization.

Main Results:

  • Identification of key public repositories for quantitative proteomics data (e.g., PRIDE).
  • Outlined critical factors for successful data (re)use.
  • Documented common challenges and potential pitfalls in quantitative data analysis.

Conclusions:

  • Public proteomics data repositories offer significant potential for novel insights.
  • Careful consideration of data quality and analysis methods is crucial for reliable results.
  • Effective reuse of quantitative proteomics data can accelerate scientific discovery.