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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...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...

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Related Experiment Video

Updated: Jun 7, 2026

Quantitation of Protein Expression and Co-localization Using Multiplexed Immuno-histochemical Staining and Multispectral Imaging
08:40

Quantitation of Protein Expression and Co-localization Using Multiplexed Immuno-histochemical Staining and Multispectral Imaging

Published on: April 8, 2016

Image analysis tools and emerging algorithms for expression proteomics.

Andrew W Dowsey1, Jane A English, Frederique Lisacek

  • 1Institute of Biomedical Engineering, Imperial College London, South Kensington, London, UK. a.w.dowsey@imperial.ac.uk

Proteomics
|November 4, 2010
PubMed
Summary
This summary is machine-generated.

Computational analysis tools are crucial for proteomics research. This study reviews bioinformatics challenges and advances in 2-DE and LC/MS techniques, highlighting areas for improved accuracy and automation in protein quantification.

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Last Updated: Jun 7, 2026

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08:40

Quantitation of Protein Expression and Co-localization Using Multiplexed Immuno-histochemical Staining and Multispectral Imaging

Published on: April 8, 2016

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Computational analysis tools have evolved significantly since the 1970s, becoming integral to expression proteomics research.
  • Established commercial packages and academic endeavors drive innovation in proteomics data analysis.
  • Image analysis pipelines are essential for interpreting complex proteomic datasets.

Purpose of the Study:

  • To describe the image analysis pipeline for 2-DE (two-dimensional electrophoresis) and LC/MS (liquid chromatography-mass spectrometry) proteomics.
  • To compare the bioinformatics challenges associated with 2-DE and LC/MS workflows.
  • To review existing commercial and academic software packages from user and technical viewpoints.

Main Methods:

  • Signal and image analysis for 2-DE protein separation.
  • Signal analysis for mass spectrometry (MS).
  • Image analysis workflow for LC/MS 'shotgun' proteomics.

Main Results:

  • Bioinformatics challenges in both 2-DE and LC/MS are identified and contrasted.
  • Existing software packages and their workflows are evaluated.
  • The importance of robust statistical methods for differential expression analysis is emphasized.

Conclusions:

  • Despite software availability, challenges in algorithm accuracy, objectivity, and automation persist.
  • Deterministic, spot-centric approaches often lead to information loss and error propagation.
  • Recent advances in signal and image analysis algorithms show promise for overcoming these limitations.