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Related Concept Videos

Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

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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...
5.6K
Mass Spectrometers01:16

Mass Spectrometers

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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:
5.8K
High-Resolution Mass Spectrometry (HRMS)01:15

High-Resolution Mass Spectrometry (HRMS)

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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...
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Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

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Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and signal-to-noise ratio for the analyte. 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 collision-induced...
1.1K
Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

854
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...
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Mass Spectrum01:23

Mass Spectrum

2.2K
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...
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Related Experiment Video

Updated: Aug 8, 2025

Whole-body Mass Spectrometry Imaging by Infrared Matrix-assisted Laser Desorption Electrospray Ionization IR-MALDESI
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Whole-body Mass Spectrometry Imaging by Infrared Matrix-assisted Laser Desorption Electrospray Ionization IR-MALDESI

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Cardinal v3 - a versatile open source software for mass spectrometry imaging analysis.

Kylie Ariel Bemis1, Melanie Christine Föll1,2,3, Dan Guo1

  • 1Khoury College of Computer Sciences, Northeastern University, Boston, USA.

Biorxiv : the Preprint Server for Biology
|March 3, 2023
PubMed
Summary
This summary is machine-generated.

Cardinal v3 is an open-source software enabling reproducible mass spectrometry imaging analysis. It offers advanced data processing, statistical analysis, and efficient handling of large datasets for comprehensive experimental workflows.

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Imaging of Biological Tissues by Desorption Electrospray Ionization Mass Spectrometry
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Whole-body Mass Spectrometry Imaging by Infrared Matrix-assisted Laser Desorption Electrospray Ionization IR-MALDESI
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Area of Science:

  • Computational Biology
  • Analytical Chemistry
  • Bioinformatics

Background:

  • Mass spectrometry imaging (MSI) experiments generate complex, high-dimensional data.
  • Reproducible analysis is crucial for validating MSI findings.
  • Existing software may not support the full range of MSI workflows or handle large datasets efficiently.

Approach:

  • Cardinal v3 is an open-source software package designed for MSI data analysis.
  • It provides a unified platform supporting diverse MSI experimental workflows.
  • The software incorporates advanced algorithms for data processing and statistical analysis.

Key Points:

  • Supports comprehensive MSI workflows, from data processing to statistical analysis.
  • Features include mass re-calibration, single-ion segmentation, and annotation-based classification.
  • Optimized for memory-efficient analysis of large-scale, multi-tissue MSI experiments.

Conclusions:

  • Cardinal v3 enhances the reproducibility and scope of mass spectrometry imaging analyses.
  • It offers powerful tools for researchers working with complex MSI data.
  • The software facilitates deeper insights from large-scale MSI studies.