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

Chemical Ionization (CI) Mass Spectrometry01:21

Chemical Ionization (CI) Mass Spectrometry

695
The molecular ion peak of a molecule in the mass spectrum provides vital information for molecular identification. However, conventional electron impact ionization can lead to the rapid dissociation of some molecular ions before they reach the detector. A milder ionization method is required to increase the lifetime of such ionized analyte molecules. Chemical ionization (CI) is a gas-phase protonation reaction useful for mass-analyzing analyte molecules that are easily protonated to yield the...
695
Mass Spectrometers01:16

Mass Spectrometers

5.2K
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:
5.2K
Electrospray Ionization (ESI) Mass Spectrometry01:12

Electrospray Ionization (ESI) Mass Spectrometry

736
Higher molecular weight biomolecules are nonvolatile compounds that may decompose before ionizing or vaporizing during mass analysis with conventional electron impact ionization methods. Accordingly, electrospray ionization (ESI) is the favored method for vaporizing and ionizing biomolecules as it circumvents rapid fragmentation and enables the recording of mass signals for the entire biomolecule.
ESI utilizes electrical energy to transfer ions from the liquid phase of the sample into the...
736
Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

4.6K
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...
4.6K
MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

4.7K
Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.
Matrix-assisted laser desorption ionization (MALDI) is a commonly...
4.7K
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

You might also read

Related Articles

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

Sort by
Same author

High-Throughput Mass Spectral Library Searching of Small Molecules in R with NIST MSPepSearch.

Journal of the American Society for Mass Spectrometry·2025
Same author

How searching against multiple libraries can lead to biased results in GC/MS-based metabolomics.

Rapid communications in mass spectrometry : RCM·2022
Same author

Multivariate Prognostic Model for Predicting the Outcome of Critically Ill Patients Using the Aromatic Metabolites Detected by Gas Chromatography-Mass Spectrometry.

Molecules (Basel, Switzerland)·2022
Same author

A general procedure for rounding m/z values in low-resolution mass spectra.

Rapid communications in mass spectrometry : RCM·2022
Same author

Predicting the absence of an unknown compound in a mass spectral database.

European journal of mass spectrometry (Chichester, England)·2019

Related Experiment Video

Updated: Jun 7, 2025

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments
08:40

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments

Published on: January 20, 2022

4.2K

The Identity Algorithm: How the Most Popular Electron Ionization Mass Spectral Library Search Engine Actually Works.

Andrey Samokhin1,2

  • 1Chemistry Department, Lomonosov Moscow State University, Moscow 119991, Russia.

Journal of the American Society for Mass Spectrometry
|November 18, 2024
PubMed
Summary

Researchers have deconstructed the ambiguous Identity algorithm used in gas chromatography/mass spectrometry (GC/MS) library searches. A new custom implementation is now available in the mssearchr R package for improved accessibility.

Keywords:
Identity algorithmR packageelectron ionizationgas chromatographymass spectrometry

More Related Videos

Photoelectron Imaging of Anions Illustrated by 310 Nm Detachment of F−
06:53

Photoelectron Imaging of Anions Illustrated by 310 Nm Detachment of F−

Published on: July 27, 2018

8.6K
Analysis of Volatile and Oxidation Sensitive Compounds Using a Cold Inlet System and Electron Impact Mass Spectrometry
05:48

Analysis of Volatile and Oxidation Sensitive Compounds Using a Cold Inlet System and Electron Impact Mass Spectrometry

Published on: September 5, 2014

9.6K

Related Experiment Videos

Last Updated: Jun 7, 2025

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments
08:40

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments

Published on: January 20, 2022

4.2K
Photoelectron Imaging of Anions Illustrated by 310 Nm Detachment of F−
06:53

Photoelectron Imaging of Anions Illustrated by 310 Nm Detachment of F−

Published on: July 27, 2018

8.6K
Analysis of Volatile and Oxidation Sensitive Compounds Using a Cold Inlet System and Electron Impact Mass Spectrometry
05:48

Analysis of Volatile and Oxidation Sensitive Compounds Using a Cold Inlet System and Electron Impact Mass Spectrometry

Published on: September 5, 2014

9.6K

Area of Science:

  • Analytical Chemistry
  • Computational Chemistry

Background:

  • The Identity algorithm in MS Search (NIST) software is crucial for gas chromatography/mass spectrometry (GC/MS) library searches.
  • Its operational details have remained unclear, hindering replication and understanding.

Purpose of the Study:

  • To deconstruct and fully understand the operational details of the Identity algorithm.
  • To develop a custom implementation that accurately replicates the original algorithm's results.

Main Methods:

  • Developed a novel approach analyzing library search results from synthetic mass spectra.
  • Tailored synthetic spectra to isolate and examine specific algorithm components.

Main Results:

  • Successfully deconstructed the Identity algorithm, revealing its complete operational logic.
  • Developed a custom implementation that precisely replicates MS Search results.
  • The custom implementation is available via the mssearchr R package.

Conclusions:

  • The ambiguity surrounding the Identity algorithm has been resolved through a unique deconstruction method.
  • The mssearchr R package provides researchers with an accessible and accurate implementation of the Identity algorithm.
  • This work enhances the reliability and reproducibility of GC/MS library searches.