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Related Concept Videos

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

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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Generation and analysis of multidimensional protein identification technology datasets.

Selene K Swanson1, Laurence Florens, Michael P Washburn

  • 1Stowers Institute for Medical Research, Kansas City, MO, USA.

Methods in Molecular Biology (Clifton, N.J.)
|February 26, 2009
PubMed
Summary

Multidimensional Protein Identification Technology (MudPIT) uses liquid chromatography and mass spectrometry to analyze complex peptide mixtures. This method provides detailed insights into proteomics with high accuracy and quantitative data.

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Mapping Dysfunctional Protein-Protein Interactions in Disease
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Published on: November 15, 2017

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09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biochemistry

Background:

  • Two-dimensional liquid chromatography (LC/LC) coupled with tandem mass spectrometry is a cornerstone of modern proteomics.
  • Multidimensional Protein Identification Technology (MudPIT) is a specific LC/LC-MS/MS system.
  • MudPIT utilizes strong cation exchange and reversed-phase chromatography in a single microcapillary column.

Purpose of the Study:

  • To describe the application of MudPIT on contemporary mass spectrometry instruments.
  • To present a data analysis pipeline for MudPIT.
  • To achieve low false positive rates and generate quantitative proteomic datasets.

Main Methods:

  • Utilizing multidimensional liquid chromatography (MudPIT) for peptide separation.
  • Coupling chromatography with tandem mass spectrometry (MS/MS).
  • Employing database searching algorithms (e.g., SEQUEST) and computational tools for data analysis.

Main Results:

  • Detailed analysis of complex peptide mixtures from various biological sources.
  • Generation of quantitative proteomic datasets.
  • Establishment of a data analysis pipeline ensuring low false positive rates.

Conclusions:

  • MudPIT is a powerful technique for in-depth proteomic analysis.
  • The described data analysis pipeline enhances the reliability and quantitation of MudPIT results.
  • This approach facilitates comprehensive understanding of proteomes from diverse biological samples.