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Mass Spectrometry: Overview

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...

Mass Spectrum: Interpretation

Mass Spectrum: Interpretation

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 soft-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...

Mass Spectrometry: Complex Analysis

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 Spectrometers

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:

Mass Spectrum

Mass Spectrum

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 number of charges 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 (the...

High-Resolution Mass Spectrometry (HRMS)

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...

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Updated: May 15, 2026

Visualization of Ambient Mass Spectrometry with the Use of Schlieren Photography

Visualization of Ambient Mass Spectrometry with the Use of Schlieren Photography

Published on: June 20, 2016

Hyperspectral visualization of mass spectrometry imaging data.

Judith M Fonville¹, Claire L Carter, Luis Pizarro

¹Biomolecular Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom.

Analytical Chemistry

|December 20, 2012

Summary

We developed a user-friendly color-coding method for mass spectrometry imaging (MSI) data. This approach enhances visualization of molecular profiles, improving biomedical research and diagnostics.

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Imaging of Biological Tissues by Desorption Electrospray Ionization Mass Spectrometry

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Visualization of Ambient Mass Spectrometry with the Use of Schlieren Photography

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Imaging of Biological Tissues by Desorption Electrospray Ionization Mass Spectrometry

Imaging of Biological Tissues by Desorption Electrospray Ionization Mass Spectrometry

Published on: July 12, 2013

Area of Science:

Biomedical research
Analytical chemistry
Data visualization

Background:

Mass spectrometry imaging (MSI) offers significant potential for biomedical diagnostics and research.
Current MSI data analysis often relies on visual interpretation of individual mass images, which can be complex and time-consuming.
A need exists for more intuitive and effective methods to visualize complex MSI datasets.

Purpose of the Study:

To develop an intuitive color-coding scheme for mass spectrometry imaging (MSI) data visualization.
To integrate automated data processing, modeling, and display for user-friendly MSI analysis.
To enable effective visualization of both spatial and molecular information within MSI datasets.

Main Methods:

Developed a color-coding scheme inspired by hyperspectral imaging methods.
Applied the color-coding to spectral characteristics, grouping similar molecular profiles under similar colors.
Utilized principal component analysis, self-organizing maps, and t-distributed stochastic neighbor embedding for data analysis.

Main Results:

Generated a single overview image from complex MSI data using the color-coding scheme.
Pixels with similar molecular profiles were displayed with similar colors, facilitating intuitive interpretation.
The visualization strategy effectively combined spatial and molecular information.

Conclusions:

The developed approach provides a user-friendly method for MSI data analysis.
This technique enhances the intuitive and effective visualization of complex MSI datasets.
The method holds promise for advancing biomedical diagnostics and research through improved data interpretation.