Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Mass Spectrometry: Alkene Fragmentation00:59

Mass Spectrometry: Alkene Fragmentation

3.6K
Alkenes lose one electron from the unsaturated π bond upon ionization and form stable molecular ions. Further fragmentation of alkenes occurs through three different reaction pathways. The most prominent fragmentation is the cleavage at the allylic position. The resultant allylic carbocation is resonance stabilized. In the mass spectra of terminal alkenes, this fragment appears at a mass-to-charge ratio of 41. In the internal alkenes, where there are two choices of allylic cleavage, the...
3.6K
Mass Spectrometry: Amine Fragmentation00:55

Mass Spectrometry: Amine Fragmentation

2.3K
Amines can be identified using mass spectroscopy based on their characteristic fragmentation patterns. The molecular ions of amines undergo fragmentation via ⍺-cleavage. The ⍺-cleavage of the carbon-carbon bonds in amines generates an alkyl radical and resonance-stabilized nitrogen-containing cation.
In amines, the number of nitrogen atoms affects the mass of the molecular ion, which is described by the nitrogen rule of mass spectrometry. This rule states that a compound containing a single...
2.3K
Mass Spectrometry: Cycloalkane Fragmentation01:05

Mass Spectrometry: Cycloalkane Fragmentation

2.3K
In mass spectrometry, cycloalkanes exhibit distinct fragmentation patterns due to the inherent stability of their molecular ions compared to linear or branched alkanes. The ring structure of cycloalkanes provides additional stability to the molecular ions, often resulting in prominent ion peaks in the mass spectrum.
For example, cyclohexane molecular ions have a mass-to-charge ratio (m/z) of 84, which tends to produce a stronger signal than linear alkanes like hexane. This stability comes from...
2.3K
Mass Spectrometry: Cycloalkene Fragmentation00:54

Mass Spectrometry: Cycloalkene Fragmentation

1.6K
The molecular ions of cycloalkenes undergo fragmentation via a retro-Diels–Alder reaction.
1.6K
Mass Spectrometry: Alkyne Fragmentation00:53

Mass Spectrometry: Alkyne Fragmentation

2.2K
The fragmentation of alkynes preferentially occurs at the carbon–carbon bond between the α and β carbon of the alkyne bond to generate a 3-propynyl cation (or propargyl cation). In terminal alkynes, there is the only type of fragmentation that yields the 3-propynyl cation. The unsubstituted 3-propynyl cation exhibits a peak at a mass-to-charge ratio of 39. In internal alkynes, the 3-propynyl cation is substituted. For example, 2-pentyne fragments into methyl-substituted 3-propynyl cation,...
2.2K
Mass Spectrometry: Alcohol Fragmentation01:03

Mass Spectrometry: Alcohol Fragmentation

4.5K
Alcohols (R-OH) ionize to lose one non-bonded electron from the oxygen atom, forming molecular ions. Due to their tendency to fragment rapidly, the intensity of the molecular ion peak in the mass spectrum is weak or sometimes absent. The fragmentation patterns for alcohols occur in two ways, i.e. ⍺-cleavage and dehydration. During ⍺-cleavage, the bond at the ⍺-position adjacent to the hydroxyl group cleaves to give a resonance-stabilized cation and a radical. However, intramolecular...
4.5K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Investigations on Multiple Protein Scaffold Filling.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same author

Explainable convolutional neural network model provides an alternative genome-wide association perspective on mutations in SARS-CoV-2.

Scientific reports·2026
Same author

EssentCell: Discovering Essential Evolutionary Relations in Noisy Single-Cell Data.

IEEE transactions on computational biology and bioinformatics·2026
Same author

Privacy-preserving federated learning with optimized ensemble weighting and knowledge distillation for COVID-19 detection from non-IID medical imaging data.

Scientific reports·2026
Same author

Global Proteomic Analysis of Colorectal Cancers Stratified by Microsatellite Instability Subtype Reveals Protein Differences.

bioRxiv : the preprint server for biology·2026
Same author

A data-driven sliding-window pairwise comparative approach for the estimation of transmission fitness of SARS-CoV-2 variants and construction of the evolution fitness landscape.

Quantitative biology (Beijing, China)·2026
Same journal

Biodegradable Self-Powered Electrotherapy Patch for Integrated Smart Wound Management.

Analytical chemistry·2026
Same journal

Metabolite Fraction Libraries for Quantitative NMR Metabolomics.

Analytical chemistry·2026
Same journal

Self-Contained Lateral-Flow Microfluidic Bead-Based Assay for Rapid Quantification of Early-Stage Kidney Biomarkers.

Analytical chemistry·2026
Same journal

Overcoming the Debye Shielding Effect with Concave-Convex Structures for Sensitivity-Enhanced Thin-Film Transistors.

Analytical chemistry·2026
Same journal

Mode-Phase-Difference Photothermal Spectroscopy Assisted by a Bent Biconically Tapered Microfiber for Gas Sensing.

Analytical chemistry·2026
Same journal

Negative-Pressure-Actuated Microfluidics: A Dual-Mode Point-of-Care Sensor for Allergen-Specific IgE in Interstitial Fluid.

Analytical chemistry·2026
See all related articles

Related Experiment Video

Updated: Feb 3, 2026

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics
09:09

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics

Published on: October 13, 2020

5.1K

Enhancing Proteoform Sequence Coverage Using Top-Down Mass Spectrometry with In-Source Fragmentation and Middle-Down

Xingzhao Xiong1, Letu Qingge2, Binhai Zhu3

  • 1Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana 70112, United States.

Analytical Chemistry
|February 2, 2026
PubMed
Summary
This summary is machine-generated.

This study enhances proteoform sequence coverage using mass spectrometry (MS). Top-down MS with in-source fragmentation and middle-down MS with partial digestion achieved over 90% coverage for complex proteins.

More Related Videos

Quantitative Metabolomics of Saccharomyces Cerevisiae Using Liquid Chromatography Coupled with Tandem Mass Spectrometry
07:25

Quantitative Metabolomics of Saccharomyces Cerevisiae Using Liquid Chromatography Coupled with Tandem Mass Spectrometry

Published on: January 5, 2021

5.0K
Quantitative Analysis of the Cellular Lipidome of Saccharomyces Cerevisiae Using Liquid Chromatography Coupled with Tandem Mass Spectrometry
08:56

Quantitative Analysis of the Cellular Lipidome of Saccharomyces Cerevisiae Using Liquid Chromatography Coupled with Tandem Mass Spectrometry

Published on: March 8, 2020

7.9K

Related Experiment Videos

Last Updated: Feb 3, 2026

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics
09:09

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics

Published on: October 13, 2020

5.1K
Quantitative Metabolomics of Saccharomyces Cerevisiae Using Liquid Chromatography Coupled with Tandem Mass Spectrometry
07:25

Quantitative Metabolomics of Saccharomyces Cerevisiae Using Liquid Chromatography Coupled with Tandem Mass Spectrometry

Published on: January 5, 2021

5.0K
Quantitative Analysis of the Cellular Lipidome of Saccharomyces Cerevisiae Using Liquid Chromatography Coupled with Tandem Mass Spectrometry
08:56

Quantitative Analysis of the Cellular Lipidome of Saccharomyces Cerevisiae Using Liquid Chromatography Coupled with Tandem Mass Spectrometry

Published on: March 8, 2020

7.9K

Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Biochemistry

Background:

  • Characterizing complex proteoforms with mutations and post-translational modifications is crucial.
  • Mass spectrometry (MS)-based techniques are advancing the study of proteoforms.
  • High proteoform sequence coverage is essential for accurate characterization.

Purpose of the Study:

  • To evaluate top-down and middle-down MS approaches for enhancing proteoform sequence coverage.
  • To assess the effectiveness of in-source fragmentation (ISF) and partial enzymatic digestion.
  • To determine if these methods can achieve high sequence coverage for complex proteins.

Main Methods:

  • Applied top-down MS with in-source fragmentation (ISF) to generate pseudo-MS3 spectra.
  • Utilized middle-down MS with short-duration enzymatic digestions to produce longer peptides.
  • Tested approaches on three model proteins: ubiquitin, myoglobin, and carbonic anhydrase II.

Main Results:

  • In-source fragmentation (ISF) in top-down MS improved sequence coverage.
  • Partial enzymatic digestion in middle-down MS yielded longer peptides, preserving proteoform information.
  • Both strategies significantly increased protein sequence coverage, exceeding 90%.

Conclusions:

  • Top-down and middle-down MS strategies effectively enhance proteoform sequence coverage.
  • ISF and partial digestion are valuable techniques for deep proteoform analysis.
  • Achieving >90% sequence coverage is feasible for complex proteoforms using these methods.