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Related Concept Videos

Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

6.4K
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...
6.4K
Mass Spectrum: Interpretation01:24

Mass Spectrum: Interpretation

1.7K
An unknown compound can be established by identifying the molecular ion peak in the mass spectrum. The molecular ion peak is often weak or absent due to the predominance of fragmentation in high-energy electron beams. In such cases, a low-energy electron beam can be used to scan the spectrum to enhance the intensity of the molecular ion peak. Additionally, chemical ionization, field ionization, and desorption ionization spectra are used to obtain a relatively intense molecular ion peak.
To...
1.7K
Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

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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...
968
Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

4.0K
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...
4.0K
Mass Spectrometers01:16

Mass Spectrometers

6.4K
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:
6.4K
Mass Spectrum01:23

Mass Spectrum

2.6K
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...
2.6K

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Related Experiment Video

Updated: Oct 5, 2025

PTR-ToF-MS Coupled with an Automated Sampling System and Tailored Data Analysis for Food Studies: Bioprocess Monitoring, Screening and Nose-space Analysis
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Data parsing in mass spectrometry imaging using R Studio and Cardinal: A tutorial.

Cameron J Shedlock1, Katherine A Stumpo1,2,3

  • 1Department of Chemistry, University of Scranton, Scranton, PA 18510, United States.

Journal of Mass Spectrometry and Advances in the Clinical Lab
|January 24, 2022
PubMed
Summary

This tutorial introduces beginners to Mass Spectrometry Imaging (MSI) data analysis using R. It provides essential guidance for navigating complex spatial and spectral data, unlocking data science potential in MSI.

Keywords:
AuNP, gold nanoparticleCardinalDESI, desorption electrospray ioniziationData validationIACUC, Institutional Animal Care and Use CommitteeITO, indium tin oxideMSI, mass spectrometry imagingMass spectrometry imagingPCA, principal component analysisR StudioRAM, random access memoryRMS, root mean squaredSNR, signal to noise ratioSSC, spatial shrunken centroidSSD, solid state driveTIC, total ion current

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Area of Science:

  • Computational chemistry
  • Data science
  • Analytical chemistry

Background:

  • Mass spectrometry imaging (MSI) is a growing field within mass spectrometry (MS).
  • MSI data analysis is challenging due to large spectral datasets and the added spatial dimension.
  • Existing R resources for MSI data are primarily for expert users, leaving a gap for beginners.

Purpose of the Study:

  • To provide a comprehensive guide for beginners to analyze Mass Spectrometry Imaging (MSI) data using R.
  • To introduce the capabilities of data science in enhancing MSI data interpretation.
  • To bridge the knowledge gap for novice users entering the field of MSI data analysis.

Main Methods:

  • Utilizing the R programming language for data analysis.
  • Demonstrating techniques for parsing and visualizing MSI data.
  • Applying data science principles to MSI datasets.

Main Results:

  • A structured tutorial approach for R-based MSI data analysis.
  • Illustrations of how data science can be applied to MSI.
  • Empowerment of beginners to analyze complex MSI data.

Conclusions:

  • R provides a powerful platform for Mass Spectrometry Imaging data analysis.
  • This tutorial serves as a foundational resource for new MSI researchers.
  • Data science approaches significantly enhance the insights gained from MSI data.