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Related Concept Videos

Tagging and Fusion Proteins01:24

Tagging and Fusion Proteins

Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...
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...

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Related Experiment Video

Updated: Jun 5, 2026

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

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

Published on: June 8, 2020

Sequence tagging reveals unexpected modifications in toxicoproteomics.

Surendra Dasari1, Matthew C Chambers, Simona G Codreanu

  • 1Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37232-0006, United States.

Chemical Research in Toxicology
|January 11, 2011
PubMed
Summary

TagRecon, a new algorithm, improves the identification of protein posttranslational modifications (PTMs) in toxicoproteomics. It effectively detects known and unexpected PTMs, outperforming existing software for analyzing complex biological samples.

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

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

Published on: June 8, 2020

Resin-Assisted Capture Coupled with Isobaric Tandem Mass Tag Labeling for Multiplexed Quantification of Protein Thiol Oxidation
07:16

Resin-Assisted Capture Coupled with Isobaric Tandem Mass Tag Labeling for Multiplexed Quantification of Protein Thiol Oxidation

Published on: June 21, 2021

Area of Science:

  • Proteomics
  • Biochemistry
  • Toxicology

Background:

  • Toxicoproteomic samples contain numerous protein posttranslational modifications (PTMs).
  • Standard database searching methods for PTM identification are computationally intensive and may miss novel modifications.
  • There is a need for efficient algorithms to accurately identify PTMs in complex toxicoproteomic datasets.

Purpose of the Study:

  • To introduce TagRecon, an advanced algorithm for identifying modified peptides in toxicoproteomic data.
  • To enhance the detection of both known and unanticipated posttranslational modifications.
  • To provide user-friendly software for analyzing mass shifts in proteomic samples.

Main Methods:

  • TagRecon utilizes inferred sequence tags to identify modified peptides.
  • A three-step strategy involves standard database searching, sequence tag-based interrogation for unexpected PTMs, and refinement searches.
  • The algorithm was tested on data from LTQ, Orbitrap, and QTOF instruments.

Main Results:

  • TagRecon identified known modifications more effectively than the MyriMatch database search engine.
  • The algorithm demonstrated superior performance in recognizing unanticipated modifications across different mass spectrometry platforms.
  • Application to toxicoproteomic data revealed unintended reagent cross-reactions and identified 25 proteins in rat liver exhibiting oxidative stress from drug exposure.

Conclusions:

  • TagRecon offers a significant advancement in identifying protein modifications within toxicoproteomic studies.
  • The developed software facilitates the detection of unexpected PTMs and mass shifts.
  • This approach highlights the utility of mining toxicoproteomic data for uncovering biologically relevant modifications and stress responses.