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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...
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called...
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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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Accurate multiplexed proteomics at the MS2 level using the complement reporter ion cluster.

Martin Wühr1, Wilhelm Haas, Graeme C McAlister

  • 1Department of Cell Biology, Harvard Medical School, Harvard University, Boston, Massachusetts 02115, United States.

Analytical Chemistry
|October 27, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces a new method for accurate quantification of tandem mass tags (TMT)-labeled peptides using MS2 scans. This approach enhances proteomic analysis by avoiding coeluting interferences without sacrificing speed or sensitivity.

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Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biochemistry

Background:

  • Isobaric labeling techniques like tandem mass tags (TMT) are powerful for quantitative proteomics.
  • However, coisolated and cofragmented interfering peptides reduce accuracy and precision in complex mixtures.
  • Existing solutions like proton-transfer ion-ion reactions (PTR) or MS3 scans decrease acquisition speed and sensitivity.

Purpose of the Study:

  • To develop a method for accurate TMT-labeled peptide quantification at the MS2 level.
  • To overcome limitations of existing methods by avoiding additional ion purification steps.
  • To improve the speed and sensitivity of quantitative proteomics.

Main Methods:

  • Quantification based on fragment ion clusters carrying TMT mass balance (complement TMT or TMT(C) ions).
  • Precursor-specific localization of TMT(C) ions minimizes interference from coeluting peptides.
  • Method implemented on high-resolution mass spectrometers (e.g., quadrupole Orbitrap).

Main Results:

  • Accurate TMT quantification achieved at the MS2 level without extra purification.
  • Complement TMT ions are precursor-specific, reducing coelution interference.
  • Method is compatible with common high-resolution mass spectrometers.
  • Potential for parallelization of multiplexed quantification, increasing throughput.

Conclusions:

  • The complement TMT ion approach offers accurate and efficient quantitative proteomics.
  • It overcomes the limitations of speed and sensitivity associated with other methods.
  • Further optimization is needed to address peptide sequence and charge state effects on TMT(C) ion formation.
  • This method holds significant potential for increasing the number of quantifiable peptides within a given time frame.