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Related Concept Videos

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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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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Tandem Mass Spectrometry01:21

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Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and signal-to-noise ratio for the analyte. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.
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Updated: Nov 7, 2025

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the

Alex Johnson1,2,3, Michael Stadlmeier1,2, Martin Wühr1,2,3

  • 1Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States.

Journal of Proteome Research
|April 30, 2021
PubMed
Summary
This summary is machine-generated.

New TMTproC technology enhances multiplexed proteomics by improving quantification accuracy and sensitivity at the MS2 level. This method expands access to high-quality multiplexed proteomics without specialized instruments.

Keywords:
CIDFAIMSTMTproaccurate quantificationcomplementary ionsinterference-freeisobaric labelingmultiplexingshotgun proteomics

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Biotechnology

Background:

  • Multiplexed proteomics enables cell state analysis but faces challenges with accurate quantification due to co-isolated peptide interference.
  • MS3-based quantification reduces interference but lowers sensitivity and requires specialized equipment.
  • Complementary ion quantification offers accurate MS2-level multiplexing compatible with standard instruments but has limitations with TMT-tags.

Purpose of the Study:

  • To evaluate and optimize complementary ion quantification using the TMTpro-tag (TMTproC) for enhanced multiplexed proteomics.
  • To assess the performance of TMTproC in terms of plexing capacity, sensitivity, and accuracy compared to existing methods.

Main Methods:

  • Utilized TMTpro-tag for complementary ion quantification, increasing multiplexing to eight channels (TMTproC).
  • Evaluated TMTproC performance against TMTpro-MS3 and real-time-search SPS-MS3 (RTS-SPS-MS3) methods.
  • Developed compatible software for TMTproC data analysis within the MaxQuant pipeline.

Main Results:

  • TMTproC demonstrated increased sensitivity, quantifying approximately 65% more proteins than TMTpro-MS3 and 18% more than RTS-SPS-MS3.
  • TMTproC exhibited superior accuracy compared to TMTpro-MS2 and RTS-SPS-MS3.
  • The TMTproC method supports eight-channel multiplexing, overcoming limitations of previous TMT-tags.

Conclusions:

  • TMTproC significantly advances multiplexed proteomics by enhancing data quality, accuracy, and sensitivity.
  • This method broadens accessibility to precise multiplexed proteomics, particularly for labs without MS3-capable instrumentation.
  • TMTproC represents a valuable tool for cell state analysis in health and disease research.