Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

8.9K
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...
8.9K
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

2.5K
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...
2.5K
Mass Spectrometry: Isotope Effect01:13

Mass Spectrometry: Isotope Effect

4.3K
Most elements exist in nature as a mixture of isotopes. The isotopes differ in weight due to their respective number of neutrons. The molecular weight of a molecule is different depending on the specific isotope of its elements involved. As a result, the mass spectrum of the molecule exhibits peaks from the same fragment at multiple positions. The positions of these mass signals depend on the mass differences between isotopes. Furthermore, the intensity of these signals is dependent on the...
4.3K
Mass Spectrometry of Amines01:15

Mass Spectrometry of Amines

5.4K
In mass spectroscopy, amines undergo fragmentation to give parent ions with odd molecule weights. This observed mass spectrum follows the nitrogen rule; a molecule with an odd number of nitrogen atoms produces a molecular ion with an odd molecular weight. Amines undergo fragmentation through α cleavage, producing nitrogen-containing cations—iminium ions—and alkyl radicals. Mass spectra of aromatic and cyclic aliphatic amines exhibit strong molecular ion peaks, but acyclic...
5.4K
Chemical Ionization (CI) Mass Spectrometry01:21

Chemical Ionization (CI) Mass Spectrometry

1.5K
The molecular ion peak of a molecule in the mass spectrum provides vital information for molecular identification. However, conventional electron impact ionization can lead to the rapid dissociation of some molecular ions before they reach the detector. A milder ionization method is required to increase the lifetime of such ionized analyte molecules. Chemical ionization (CI) is a gas-phase protonation reaction useful for mass-analyzing analyte molecules that are easily protonated to yield the...
1.5K
Mass Spectrometry: Alkene Fragmentation00:59

Mass Spectrometry: Alkene Fragmentation

3.6K
Alkenes lose one electron from the unsaturated π bond upon ionization and form stable molecular ions. Further fragmentation of alkenes occurs through three different reaction pathways. The most prominent fragmentation is the cleavage at the allylic position. The resultant allylic carbocation is resonance stabilized. In the mass spectra of terminal alkenes, this fragment appears at a mass-to-charge ratio of 41. In the internal alkenes, where there are two choices of allylic cleavage, the...
3.6K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Uncovering the Risk: Incidence of Upper Tract Urothelial Carcinoma Following Renal Transplantation in the Netherlands.

European urology open science·2025
Same author

A Cutaneous Vascular Neoplasm With an EWSR1-NFATC2 Translocation-Contributing to the Spectrum of Vascular Lesions Characterized by NFATC-Related Fusions.

Journal of cutaneous pathology·2025
Same author

Contrast-enhanced Ultrasound Imaging Following Transperineal Laser Ablation for Lower Urinary Tract Symptoms.

Urology·2024
Same author

Outcomes of CEM43 in Predicting Thermal Damage Induced by Focal Laser Ablation in Controlled Ex Vivo Experiments: A Comparison to Histology and MRI.

Lasers in surgery and medicine·2024
Same author

Quantification of fluorescence angiography for visceral perfusion assessment: measuring agreement between two software algorithms.

Surgical endoscopy·2024
Same author

Cardiac thrombus dissolution in acute ischemic stroke: A substudy of Mind the Heart.

Heliyon·2023

Related Experiment Video

Updated: Feb 3, 2026

Sample Preparation Strategies for Mass Spectrometry Imaging of 3D Cell Culture Models
08:14

Sample Preparation Strategies for Mass Spectrometry Imaging of 3D Cell Culture Models

Published on: December 5, 2014

18.7K

Strategies for managing multi-patient 3D mass spectrometry imaging data.

D R N Vos1, I Jansen2, M Lucas3

  • 1The Maastricht Multimodal Molecular Imaging Institute (M4I), Maastricht University, 6229 ER Maastricht, the Netherlands.

Journal of Proteomics
|October 22, 2018
PubMed
Summary

Mass spectrometry imaging (MSI) reveals compound localization in tumors. This study shows that 33% of a tissue sample must be measured using 3D MALDI-MSI to overcome sampling bias and ensure accurate bladder cancer biomarker discovery.

Keywords:
3-dimensionalBladder cancerFormalin-fixed paraffin-embedded tissueMass spectrometry imagingSampling bias

More Related Videos

MALDI Imaging Mass Spectrometry of Neuropeptides in Parkinson's Disease
16:57

MALDI Imaging Mass Spectrometry of Neuropeptides in Parkinson's Disease

Published on: February 14, 2012

26.9K
Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics
09:09

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics

Published on: October 13, 2020

5.1K

Related Experiment Videos

Last Updated: Feb 3, 2026

Sample Preparation Strategies for Mass Spectrometry Imaging of 3D Cell Culture Models
08:14

Sample Preparation Strategies for Mass Spectrometry Imaging of 3D Cell Culture Models

Published on: December 5, 2014

18.7K
MALDI Imaging Mass Spectrometry of Neuropeptides in Parkinson's Disease
16:57

MALDI Imaging Mass Spectrometry of Neuropeptides in Parkinson's Disease

Published on: February 14, 2012

26.9K
Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics
09:09

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics

Published on: October 13, 2020

5.1K

Area of Science:

  • Biomedical Research
  • Analytical Chemistry
  • Oncology

Background:

  • Mass spectrometry imaging (MSI) is crucial for localizing metabolites and proteins in diseased tissues like tumors.
  • Current MSI applications, including 2D and 3D imaging, can introduce sampling bias at sample or patient levels.
  • Understanding sampling bias is essential for accurate biomarker discovery in complex diseases.

Purpose of the Study:

  • To investigate the impact of sampling bias on sample representativeness.
  • To assess the effect of sampling bias on the precision of biomarker discovery for bladder cancer histological grading using MSI.
  • To evaluate the utility of 3D matrix-assisted laser desorption/ionization (MALDI) MSI for analyzing formalin-fixed paraffin-embedded (FFPE) bladder cancer tissues.

Main Methods:

  • Formalin-fixed paraffin-embedded (FFPE) tissues from 14 bladder cancer patients were analyzed using 3D MALDI-MSI.
  • Novel outlier detection routines were applied to 3D-MSI data, evaluating digestion efficacy and z-directed regression.
  • Data preprocessing involved removing 20% of outlier data before analysis.

Main Results:

  • An average of 33% of a tissue sample requires measurement to adequately cover biological variance.
  • Outlier detection routines improved the reliability of 3D-MSI data analysis.
  • Sampling bias significantly influences result variability, particularly in smaller patient cohorts.

Conclusions:

  • 3D MALDI-MSI can be effectively applied to FFPE bladder cancer tissues, demonstrating reproducibility with optimized protocols.
  • Addressing sampling bias is critical for precise biomarker discovery in multi-patient MSI studies.
  • The presented data analysis workflow offers a pipeline for multi-patient 3D FFPE-MSI studies.