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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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Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
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Author Spotlight: Quantitative Detection of DNA Protein Crosslinks and Their Post-Translational Modifications
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Software eyes for protein post-translational modifications.

Seungjin Na1, Eunok Paek

  • 1Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, 92093; Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA, 92093.

Mass Spectrometry Reviews
|June 4, 2014
PubMed
Summary

Identifying post-translational modifications (PTMs) is challenging. This study presents faster computational methods for PTM analysis using tandem mass spectrometry (MS/MS), including disulfide bond identification.

Keywords:
computational proteomicspost-translational modificationsoftwaretandem mass spectrometry

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Area of Science:

  • Proteomics and Computational Biology
  • Biochemistry and Molecular Biology

Background:

  • Post-translational modifications (PTMs) are essential cellular regulatory mechanisms.
  • Identifying PTMs using tandem mass spectrometry (MS/MS) is a significant challenge in proteomics.
  • Traditional database search tools are slow for large-scale PTM analysis.

Purpose of the Study:

  • To present recent computational developments for PTM identification.
  • To enhance the speed and scope of PTM analysis from MS/MS data.
  • To address computational challenges in identifying multiply modified peptides and disulfide bonds.

Main Methods:

  • Review of computational strategies for PTM identification.
  • Discussion of algorithms for accelerating database searches.
  • Presentation of methods for analyzing complex PTMs like disulfide linkages.

Main Results:

  • Development of faster computational approaches for PTM discovery.
  • Improved methods for identifying peptides with multiple modifications.
  • Dedicated software solutions for disulfide bond identification.

Conclusions:

  • Computational advancements are crucial for efficient PTM identification.
  • Faster and more comprehensive PTM analysis is now feasible.
  • Specialized methods are required for non-covalent PTMs like disulfide bonds.