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

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

6.4K
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...
6.4K
High-Resolution Mass Spectrometry (HRMS)01:15

High-Resolution Mass Spectrometry (HRMS)

1.3K
The resolution of a mass spectrometer depends on the efficiency of separating ions with different ion masses. The mass of an atom is approximated to the sum of the masses of protons and neutrons inside, considering the masses of protons and neutrons as equal. However, the masses of the proton (1.6726 × 10−24 g) and neutron (1.6749 × 10−24 g) are not truly equal. There is a minor error in the expression of atomic masses relative to the simplest atom of hydrogen. For...
1.3K
Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

747
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...
747
Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

5.1K
Mass spectrometry is an analytical technique used to determine the molecular mass and molecular formula of a compound. The basic principle of mass spectrometry is to generate ions from the analyte molecule and measure these ion abundances against their molecular mass.  One common type of ionization, known as electrospray ionization or EI, bombards the analyte molecules in the gas phase with high-energy electron beams. The electron beams displace an electron from the molecule and leave...
5.1K
Mass Spectrum01:23

Mass Spectrum

1.9K
A mass spectrum is the graphical representation of the relative abundance of the charged fragments in an analyte plotted against their mass-to-charge ratio (m/z). The plot's x axis represents the ratio of the mass of the charged fragment to the elementary charge it carries. The y axis of the plot represents the relative abundance of each charged species. The relative abundance is calculated from the signal intensity of each charged species recorded at the detector. The most intense signal...
1.9K
Matrix-Assisted Laser Desorption Ionization (MALDI)01:08

Matrix-Assisted Laser Desorption Ionization (MALDI)

301
Matrix-assisted laser desorption ionization (MALDI) is a powerful analytical technique used in mass spectrometry. It enables the identification and characterization of various biomolecules, including proteins, peptides, nucleic acids, and carbohydrates. MALDI spectrometry is widely employed in biological and medical research, as well as in fields like pharmacology and biochemistry.
The analyte of interest, a biomolecule or a mixture of biomolecules, is mixed with a suitable matrix material. The...
301

You might also read

Related Articles

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

Sort by
Same author

Agentic AI for Structural Elucidation and Discovery of Drug Metabolites from Mass Spectrometry Data.

bioRxiv : the preprint server for biology·2026
Same author

MALDI Tandem Mass Spectrometry for Colony-Based Dereplication of Natural Products.

bioRxiv : the preprint server for biology·2026
Same author

The Distribution of Xenobiotics of Terrigenous Origin in the Nearshore Waters of a Caribbean Island.

Environmental science & technology·2026
Same author

Early seed priming with closely related <i>Bacillus</i> strains induces divergent physiological and defense responses in melon.

Horticulture research·2026
Same author

Predicting Discrete Structural Transformations in Small Molecules from Tandem Mass Spectrometry.

bioRxiv : the preprint server for biology·2026
Same author

Conversion of CO<sub>2</sub> into valuable products: engineering the PirC-PGAM switch in cyanobacteria to direct carbon flux into desired products.

Microbial cell factories·2026
Same journal

How "Soft" Are Your Gas Mixtures? Effects of Modifier Gas Types on the Dissociation of Labile Ions in Differential Mobility Spectrometry.

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

A Robotic Sample Handling Platform for Fully Automated Nanospray Desorption Electrospray Ionization Mass Spectrometry Imaging.

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

Direct Analysis in Real-Time Tandem Mass Spectrometry for Rapid Screening of Thirty-one Plant Growth Regulator Residues in <i>Rehmannia glutinosa</i>.

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

Characterization of Alkane Oxidation Products in a Corona-Discharge Reactor Using Ammonia-Doped Ion Mobility-Mass Spectrometry.

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

Integration of a Modified Synchrotron Radiation Photoionization Time-of-Flight Mass Spectrometer with a Residual Gas Analyzer for Complementary Detection of Catalytic Products with Different Ionization Energies.

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

Screen for Tissue-Specific Markers of Drug-Induced Phospholipidosis Using Mass Spectrometry Imaging.

Journal of the American Society for Mass Spectrometry·2026
See all related articles

Related Experiment Video

Updated: Jun 24, 2025

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
12:11

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

6.8K

ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization.

Mohammad Reza Zare Shahneh1, Michael Strobel1, Giovanni Andrea Vitale2

  • 1Department of Computer Science and Engineering, University of California Riverside, 900 University Ave., Riverside, California 92521, United States.

Journal of the American Society for Mass Spectrometry
|June 3, 2024
PubMed
Summary
This summary is machine-generated.

ModiFinder identifies structural modifications in small molecules using tandem mass spectrometry (MS/MS) data. This computational tool precisely localizes modifications, accelerating the discovery of novel compounds.

More Related Videos

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
10:01

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

19.7K
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

11.9K

Related Experiment Videos

Last Updated: Jun 24, 2025

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
12:11

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

6.8K
Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
10:01

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

19.7K
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

11.9K

Area of Science:

  • Analytical Chemistry
  • Computational Chemistry
  • Metabolomics

Background:

  • Untargeted tandem mass spectrometry (MS/MS) is a high-throughput method for small molecule analysis.
  • Computational methods like MS/MS library search, analog library search, and molecular networking aid in compound identification.
  • Automated methods for site-specific structural modification information in MS/MS data are lacking.

Purpose of the Study:

  • To introduce ModiFinder, a novel computational tool for localizing structural modifications in small molecules.
  • To leverage MS/MS spectral peak alignment between known and unknown compounds to identify modification sites.
  • To enhance the capabilities of MS/MS analog searching and molecular networking for novel compound discovery.

Main Methods:

  • ModiFinder aligns MS/MS spectra of structurally related known and unknown small molecules.
  • It focuses on shifted MS/MS fragment peaks to identify substructures containing modifications.
  • The tool synthesizes peak alignment information to score the likelihood of modification sites on known molecules.

Main Results:

  • ModiFinder effectively localizes structural modifications in small molecules.
  • The method enhances the identification of unknown compounds by pinpointing modification sites.
  • Demonstrated utility in accelerating the discovery of novel chemical entities.

Conclusions:

  • ModiFinder provides site-specific information on structural modifications, a previously unmet need in MS/MS data analysis.
  • This tool significantly advances the capabilities of analog searching and molecular networking.
  • ModiFinder is poised to accelerate the discovery of novel compounds through improved structural elucidation.