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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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Western Blotting01:15

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Western blotting is an analytical technique for protein identification. It has various applications in immunology and medicine, including detecting diseases like bovine spongiform encephalopathy, mad cow disease, and human and feline immunodeficiency virus from biological samples.
The technique begins with separating proteins from the sample using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), followed by protein transfer, immunoblotting, and finally, protein detection.
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Related Experiment Video

Updated: Oct 29, 2025

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Quantification of Changes in Protein Expression Using SWATH Proteomics.

Clarissa Braccia1, Nara Liessi2, Andrea Armirotti3

  • 1D3 Pharmachemistry, Istituto Italiano di Tecnologia, Genova, Italy.

Methods in Molecular Biology (Clifton, N.J.)
|July 8, 2021
PubMed
Summary
This summary is machine-generated.

Sequential Window Acquisition of all Theoretical fragment ion spectra (SWATH) enables accurate protein quantification. This data-independent acquisition method, utilizing ion libraries, streamlines proteomics data analysis from sample prep to results.

Keywords:
High-resolution LC-MS/MSIon libraryMultivariate data analysisQuantitative proteomicsSWATH

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Biotechnology

Background:

  • Accurate protein quantification is crucial in biological research.
  • Data-independent acquisition methods offer advantages in comprehensive analysis.
  • Sequential Window Acquisition of all Theoretical fragment ion spectra (SWATH) is a powerful technique.

Purpose of the Study:

  • To describe a typical workflow for SWATH experiments.
  • To provide guidance on sample preparation and data analysis for SWATH.
  • To highlight the capabilities of SWATH for large-scale protein quantification.

Main Methods:

  • Utilizing Sequential Window Acquisition of all Theoretical fragment ion spectra (SWATH) acquisition.
  • Employing fast scanning hybrid mass spectrometers.
  • Leveraging ion libraries for spectral and chromatographic data.

Main Results:

  • SWATH enables accurate quantification of thousands of proteins in a single run.
  • The method demonstrates high accuracy, reproducibility, and sensitivity.
  • A complete workflow from sample preparation to data analysis is presented.

Conclusions:

  • SWATH is an effective data-independent acquisition strategy for deep proteomics.
  • The described workflow facilitates robust protein quantification.
  • This approach enhances biological sample analysis through mass spectrometry.