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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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Protein Modifications in the RER01:26

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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.
Broadly, these modifications can be categorized into four main categories — glycosylation, formation of disulfide bonds, assembly of protein subunits, and specific proteolytic cleavages like removal of signal...
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Export of Misfolded Proteins out of the ER01:32

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After folding, the ER assesses the quality of secretory and membrane proteins. The correctly folded proteins are cleared by the calnexin cycle for transport to their final destination, while misfolded proteins are held back in the ER lumen. The ER chaperones attempt to unfold and refold the misfolded proteins but sometimes fail to achieve the correct native conformation. Such terminally misfolded proteins are then exported to the cytosol by ER-associated degradation or ERAD pathway for...
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Proteins: From Genes to Degradation02:11

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Within a biological system, the DNA encodes the RNA, and the nucleotide sequence in the RNA further defines the amino acid sequence in the protein. This is referred to as “The Central Dogma of Molecular Biology” - a term coined by Francis Crick.  Central dogma is a firm principle in biology that defines the flow of genetic information within any life form. The two fundamental steps in central dogma are - transcription and translation.
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Ribosome Profiling02:24

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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
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Characterization of Proteoforms with Unknown Post-translational Modifications Using the MIScore.

Qiang Kou1, Binhai Zhu2, Si Wu3

  • 1Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis , Indianapolis, Indiana 46202, United States.

Journal of Proteome Research
|June 14, 2016
PubMed
Summary
This summary is machine-generated.

This study introduces the Modification Identification Score (MIScore) for automated proteoform characterization. The Bayesian-based MIScore accurately identifies and localizes post-translational modifications (PTMs) in top-down mass spectrometry data.

Keywords:
post-translational modificationproteoform

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Utilizing a Comprehensive Immunoprecipitation Enrichment System to Identify an Endogenous Post-translational Modification Profile for Target Proteins
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Area of Science:

  • Proteomics and Mass Spectrometry
  • Biochemistry and Molecular Biology

Background:

  • Proteoforms, generated by genetic variations, alternative splicing, and post-translational modifications (PTMs), present complex challenges in biological research.
  • Top-down mass spectrometry is a key technology for analyzing intact proteins and identifying multiple primary structure alterations (PSAs) in proteoforms.
  • Current proteoform identification relies on database searching, often leading to incomplete characterization due to unannotated PSAs, necessitating manual annotation.

Purpose of the Study:

  • To develop an automated method for identifying and localizing post-translational modifications (PTMs) in proteoforms.
  • To improve the characterization of proteoforms identified through top-down mass spectrometry.
  • To reduce reliance on manual annotation for proteoform analysis.

Main Methods:

  • Development and application of the Modification Identification Score (MIScore), a Bayesian model-based algorithm.
  • Utilizing top-down mass spectrometry data for proteoform analysis.
  • Experimental validation of MIScore's performance in identifying and localizing PTMs.

Main Results:

  • The MIScore demonstrates high accuracy in identifying and localizing post-translational modifications (PTMs) within proteoforms.
  • The method is effective for characterizing proteoforms with one or two modifications.
  • Successful automation of PTM identification and localization, reducing manual effort.

Conclusions:

  • The Modification Identification Score (MIScore) offers a robust and accurate automated solution for proteoform characterization.
  • MIScore enhances the efficiency and reliability of analyzing complex proteoforms using top-down mass spectrometry.
  • This approach facilitates deeper insights into proteoform diversity and function.