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

Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

1.8K
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.
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 collision-induced...
1.8K
Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

4.8K
The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can occur at...
4.8K
Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation01:01

Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation

2.0K
The fragmentation patterns observed for compounds such as carboxylic acids, esters, and amides in the mass spectra include ⍺-cleavage and McLafferty rearrangement. Fragmentation by ⍺-cleavage preferentially occurs at the carbon-carbon bond at the ⍺-position next to the carboxylic group to generate a neutral radical and a cation. Long chain compounds with hydrogen at their γ-carbon undergo McLafferty rearrangement to give a radical cation and a neutral alkene.
For example, the...
2.0K
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

7.6K
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...
7.6K
Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

1.3K
Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
1.3K
Mass Spectrometers01:16

Mass Spectrometers

7.7K
This lesson details the instrumentation of a mass spectrometer—a physical instrument to perform mass spectrometry on analyte molecules and record the characteristic mass spectra. This is achieved via three chief functions:
7.7K

You might also read

Related Articles

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

Sort by
Same author

Cryo-EM provides insight into how the <i>Staphylococcus aureus</i> IsdH receptor removes hemin from the hemoglobin:haptoglobin complex.

bioRxiv : the preprint server for biology·2026
Same author

Cross-Platform Assessment of Sub-50 nm Nanopipette Emitters for Native Electrospray Ionization Mass Spectrometry.

bioRxiv : the preprint server for biology·2026
Same author

Visual exoproteomics of <i>Clostridium thermocellum</i> during anaerobic biomass-degradation identifies functional spirosomes.

bioRxiv : the preprint server for biology·2026
Same author

CIPHER: An end-to-end framework for designing optimized aggregated spatial transcriptomics experiments.

PLoS computational biology·2026
Same author

Science for the Masses.

Journal of the American Society for Mass Spectrometry·2026
Same author

Mass spectrometry structural analysis of intrinsically disordered phosphoproteins.

International journal of mass spectrometry·2026

Related Experiment Video

Updated: Nov 15, 2025

Analyzing Large Protein Complexes by Structural Mass Spectrometry
15:35

Analyzing Large Protein Complexes by Structural Mass Spectrometry

Published on: June 19, 2010

24.5K

ClipsMS: An Algorithm for Analyzing Internal Fragments Resulting from Top-Down Mass Spectrometry.

Carter Lantz1, Muhammad A Zenaidee1, Benqian Wei1

  • 1Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States.

Journal of Proteome Research
|March 2, 2021
PubMed
Summary

A new algorithm, ClipsMS, assigns both terminal and internal fragments in top-down mass spectrometry (TD-MS) data. This method enhances protein sequence coverage and modification site localization, improving TD-MS analysis.

Keywords:
electron capture dissociation (ECD)internal fragmentterminal fragmenttop-down mass spectrometry (TD-MS)

More Related Videos

Identification of RNA Fragments Resulting from Enzymatic Degradation using MALDI-TOF Mass Spectrometry
09:20

Identification of RNA Fragments Resulting from Enzymatic Degradation using MALDI-TOF Mass Spectrometry

Published on: April 11, 2022

3.6K
A Simple Fractionated Extraction Method for the Comprehensive Analysis of Metabolites, Lipids, and Proteins from a Single Sample
11:17

A Simple Fractionated Extraction Method for the Comprehensive Analysis of Metabolites, Lipids, and Proteins from a Single Sample

Published on: June 1, 2017

36.0K

Related Experiment Videos

Last Updated: Nov 15, 2025

Analyzing Large Protein Complexes by Structural Mass Spectrometry
15:35

Analyzing Large Protein Complexes by Structural Mass Spectrometry

Published on: June 19, 2010

24.5K
Identification of RNA Fragments Resulting from Enzymatic Degradation using MALDI-TOF Mass Spectrometry
09:20

Identification of RNA Fragments Resulting from Enzymatic Degradation using MALDI-TOF Mass Spectrometry

Published on: April 11, 2022

3.6K
A Simple Fractionated Extraction Method for the Comprehensive Analysis of Metabolites, Lipids, and Proteins from a Single Sample
11:17

A Simple Fractionated Extraction Method for the Comprehensive Analysis of Metabolites, Lipids, and Proteins from a Single Sample

Published on: June 1, 2017

36.0K

Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Bioinformatics

Background:

  • Top-down mass spectrometry (TD-MS) is crucial for protein sequence analysis.
  • Assigning only terminal fragments limits sequence coverage and modification site identification.
  • Computational challenges hinder the assignment of internal fragments in TD-MS.

Purpose of the Study:

  • To introduce ClipsMS, a novel algorithm for assigning both terminal and internal fragments in TD-MS.
  • To demonstrate ClipsMS's capability in locating protein modifications.
  • To improve sequence coverage and data interpretation in TD-MS.

Main Methods:

  • Development and application of the ClipsMS algorithm.
  • Analysis of top-down mass spectrometry data for apo-myoglobin and oxidized apo-myoglobin.
  • Utilizing ClipsMS for fragment ion assignment and modification site mapping.

Main Results:

  • ClipsMS successfully assigns both terminal and internal fragments from TD-MS.
  • Inclusion of internal fragments increased sequence coverage for apo-myoglobin to 78%.
  • ClipsMS accurately confirmed oxidation sites on methionine residues in oxidized apo-myoglobin.

Conclusions:

  • Internal fragments significantly enhance information extraction from TD-MS data.
  • ClipsMS is a valuable tool for comprehensive analysis of top-down mass spectra.
  • The algorithm facilitates accurate protein sequencing and post-translational modification site identification.