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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...
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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Related Experiment Video

Updated: Jun 13, 2026

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry
10:05

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry

Published on: October 24, 2018

Deep Proteoform Sequencing with Top-Down Direct Mass Technology.

Kenneth R Durbin1,2, Taojunfeng Su3, Ryan T Fellers1,2,3

  • 1Proteinaceous, Inc., Evanston, IL, 60201, United States.

Biorxiv : the Preprint Server for Biology
|June 12, 2026
PubMed
Summary
This summary is machine-generated.

Individual Ion Mass Spectrometry (I²MS) with Direct Mass Technology mode (DMTm) enhances protein analysis by improving sensitivity and resolution. This new workflow enables deep proteoform sequencing, significantly increasing sequence coverage for large proteins.

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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

Related Experiment Videos

Last Updated: Jun 13, 2026

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry
10:05

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry

Published on: October 24, 2018

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
10:37

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

Published on: November 15, 2017

Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Biochemistry

Background:

  • Conventional top-down mass spectrometry faces limitations in resolving overlapping isotopic distributions, hindering deep proteoform sequencing.
  • Orbitrap mass spectrometers offer advanced capabilities for protein analysis, but further improvements in sensitivity, resolution, and mass range are desirable.

Purpose of the Study:

  • To present an end-to-end workflow for deep proteoform sequencing using top-down mass spectrometry with Individual Ion Mass Spectrometry (I²MS) and Direct Mass Technology mode (DMTm).
  • To demonstrate the enhanced performance of DMTm compared to conventional top-down mass spectrometry methods across various fragmentation modes.
  • To introduce Proteoform Studio, a software platform for optimized ion processing and data integration to achieve comprehensive sequence coverage.

Main Methods:

  • Utilized Individual Ion Mass Spectrometry (I²MS) with Direct Mass Technology mode (DMTm) on an Orbitrap mass spectrometer.
  • Assigned charge of individual fragment ions and converted spectra from m/z to the mass domain to resolve isotopic distributions.
  • Employed multiple fragmentation modes and integrated data from DMTm and conventional top-down methods using Proteoform Studio.

Main Results:

  • Top-down DMTm significantly outperformed conventional methods, increasing sequence coverage for a glycosylated antibody heavy chain from 27.5% to 83.3% in 10 minutes.
  • Achieved near-complete coverage (>95%) of the internal region of a large protein, a region previously difficult to characterize.
  • Combined DMTm and conventional top-down data yielded 90.2% heavy chain sequence coverage, demonstrating complementary fragmentation patterns.

Conclusions:

  • The developed top-down DMTm workflow enables substantially deeper proteoform sequencing with improved sensitivity, resolution, and mass range.
  • Proteoform Studio facilitates comprehensive sequence coverage by optimizing ion processing and integrating data from complementary methods.
  • This straightforward and complete workflow confidently defines proteoforms in biological systems and aids biotherapeutic development.