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Related Concept Videos

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:
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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...
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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...
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Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
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Mass Analyzers: Overview01:13

Mass Analyzers: Overview

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The mass analyzer is a crucial component of the mass spectrometer. In the ionization chamber, the vaporized sample is bombarded with a high-energy electron beam to generate a radical cation and further fragment into neutral molecules, radicals, and cations. A series of negatively charged accelerator plates accelerate the cations into the mass analyzer. The mass analyzer separates ions according to their mass-to-charge (m/z) ratios and then directs them to the detector. The common types of mass...
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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...
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Updated: Jul 10, 2025

Sample Preparation Strategies for Mass Spectrometry Imaging of 3D Cell Culture Models
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Cardinal v.3: 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, MA, USA.

Nature Methods
|November 23, 2023
PubMed
Summary
This summary is machine-generated.

Cardinal v.3 is open-source software for reproducible mass spectrometry imaging analysis. This major update enhances data processing, statistical analysis, and memory efficiency for large experiments.

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Area of Science:

  • Computational Biology
  • Analytical Chemistry
  • Biotechnology

Background:

  • Mass spectrometry imaging (MSI) is a powerful technique for spatial molecular analysis.
  • Reproducible and efficient analysis of MSI data is crucial for scientific advancement.
  • Existing software may have limitations in handling complex MSI workflows and large datasets.

Purpose of the Study:

  • To introduce Cardinal v.3, a significant update to open-source software for MSI data analysis.
  • To provide a comprehensive tool supporting diverse MSI experimental workflows.
  • To enhance reproducibility and efficiency in MSI data analysis.

Main Methods:

  • Cardinal v.3 offers advanced data processing, including mass recalibration.
  • It incorporates sophisticated statistical analyses like single-ion segmentation and annotation-based classification.
  • The software is designed for memory-efficient analysis of large-scale, multitissue MSI experiments.

Main Results:

  • Cardinal v.3 supports a wide range of mass spectrometry imaging workflows.
  • The updated software facilitates advanced data processing and statistical analysis.
  • It enables efficient handling of large-scale MSI datasets, improving analytical capabilities.

Conclusions:

  • Cardinal v.3 represents a major advancement in open-source software for reproducible MSI analysis.
  • The software's enhanced capabilities support complex MSI workflows and large datasets.
  • It is a valuable tool for researchers in computational biology and analytical chemistry.