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Related Concept Videos

Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

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...
Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

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 electron 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 behind a...
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. 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...
MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

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

High-Resolution Mass Spectrometry (HRMS)

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 example, the mass of helium...
Mass Spectrometers01:16

Mass Spectrometers

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:

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Capturing Small Molecule Communication Between Tissues and Cells Using Imaging Mass Spectrometry
07:58

Capturing Small Molecule Communication Between Tissues and Cells Using Imaging Mass Spectrometry

Published on: April 3, 2019

Computational mass spectrometry for small molecules.

Kerstin Scheubert1, Franziska Hufsky, Sebastian Böcker

  • 1Chair of Bioinformatics, Friedrich Schiller University, Ernst-Abbe-Platz 2, Jena, Germany. kerstin.scheubert@uni-jena.de.

Journal of Cheminformatics
|March 5, 2013
PubMed
Summary
This summary is machine-generated.

Identifying small molecules in mass spectrometry (MS) data is challenging. This review details computational methods for compound identification, from spectral library searching to structural elucidation of unknowns using MS data.

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Integrated Cell Manipulation Platform Coupled with the Single-probe for Mass Spectrometry Analysis of Drugs and Metabolites in Single Suspension Cells
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Improved Polymerase Chain Reaction-restriction Fragment Length Polymorphism Genotyping of Toxic Pufferfish by Liquid Chromatography/Mass Spectrometry
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Last Updated: May 13, 2026

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Published on: September 20, 2016

Area of Science:

  • Analytical Chemistry
  • Computational Chemistry
  • Bioinformatics

Background:

  • Mass spectrometry (MS) is crucial for analyzing small molecules.
  • Interpreting MS data for small molecule identification presents significant computational challenges.
  • Accurate identification is vital for various scientific disciplines, including metabolomics and drug discovery.

Purpose of the Study:

  • To provide a comprehensive overview of computational strategies for small molecule identification from MS data.
  • To discuss methods for searching spectral libraries and elucidating unknown compound structures.
  • To highlight available software tools for different stages of the MS data analysis pipeline.

Main Methods:

  • Spectral library searching: principles and limitations.
  • Molecular formula determination using isotope pattern analysis.
  • De novo analysis of fragmentation spectra via fragmentation trees.
  • Computational approaches for metabolic network reconstruction from MS data.

Main Results:

  • Detailed explanation of spectral library searching pitfalls.
  • Overview of techniques for molecular formula identification.
  • Discussion of automated methods for compounds absent in spectral libraries.
  • Insight into de novo structural elucidation using fragmentation patterns.

Conclusions:

  • Computational methods are essential for overcoming challenges in small molecule identification from MS data.
  • A range of techniques exist, from library matching to de novo structure elucidation.
  • Software tools are available to support the entire MS data analysis workflow for small molecules.