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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...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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 form...
Subcellular Fractionation01:32

Subcellular Fractionation

The homogenate obtained after cell lysis contains various membrane-bound organelles that can be further separated into pure fractions by subcellular fractionation. These isolates are used to study specific cellular components, analyze localized protein activity, and are even employed in diagnostics. Fractionation is typically achieved using centrifugation methods, the most common being density-gradient and differential centrifugation.
Differential Centrifugation
Differential centrifugation is...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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 form...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Distribution of Cytoplasmic Content02:33

Distribution of Cytoplasmic Content

Cytokinesis segregates a cell’s chromosomes and organelles into its daughter cells. Organelles divide and grow prior to cell division but cannot be synthesized de novo; therefore, cells must receive at least one copy of each organelle to survive. Currently, many of the details of how the organelles are distributed are not yet fully elucidated.
Distribution of cytoplasmic determinants
The cytoplasm contains various organelles, as well as salts, proteins, and water. The distribution of small...

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Related Experiment Video

Updated: Jun 6, 2026

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

Published on: May 9, 2017

Tranche distributed repository and ProteomeCommons.org.

Bryan E Smith1, James A Hill, Mark A Gjukich

  • 1Departments of Biological Chemistry, Bioinformatics and Chemistry, University of Michigan, Ann Arbor, MI, USA. besmit@umich.edu

Methods in Molecular Biology (Clifton, N.J.)
|November 11, 2010
PubMed
Summary
This summary is machine-generated.

Tranche and ProteomeCommons.org offer a secure, distributed data repository for proteomics researchers. These platforms ensure data integrity, provenance, and controlled access, supporting open science initiatives.

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TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis
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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

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Last Updated: Jun 6, 2026

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

Published on: May 9, 2017

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis
07:44

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

Area of Science:

  • Proteomics
  • Bioinformatics
  • Data Archiving

Background:

  • The proteomics community requires robust solutions for managing and disseminating large datasets.
  • Ensuring data integrity, provenance, and controlled access is crucial for scientific reproducibility.
  • Existing data archiving solutions face challenges in supporting open access while maintaining data security.

Purpose of the Study:

  • To introduce Tranche, a distributed data repository for proteomics.
  • To highlight the integration of Tranche with ProteomeCommons.org for enhanced research capabilities.
  • To discuss the importance of public data availability and the challenges of open access in data archiving.

Main Methods:

  • Development of a distributed repository (Tranche) with features for large file support, access controls, and licensing.
  • Integration with an online community resource (ProteomeCommons.org) offering project management and annotation tools.
  • Provision of technical overviews and user instructions for graphical user interface (GUI), command-line tools, and Application Programmer Interface (API).

Main Results:

  • Tranche provides a secure and redundant storage and dissemination system for proteomics data.
  • The platform facilitates data provenance and integrity.
  • Integration with ProteomeCommons.org enhances usability and community engagement for proteomics researchers.

Conclusions:

  • Tranche and ProteomeCommons.org offer a valuable integrated solution for proteomics data management and sharing.
  • The platforms address key challenges in data archiving, promoting open access while ensuring data security and provenance.
  • Future development efforts aim to further enhance these resources for the proteomics community.