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

MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

7.5K
Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.Matrix-assisted laser desorption ionization (MALDI) is a commonly...
7.5K
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

3.0K
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...
3.0K
Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

2.1K
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...
2.1K
Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

10.4K
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 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...
10.4K
Mass Spectrometers01:16

Mass Spectrometers

10.9K
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:
10.9K
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

8.8K
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...
8.8K

You might also read

Related Articles

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

Sort by
Same author

The Interplay between Gut Microbiota and Diet-Induced Kidney Protection.

Kidney360·2026
Same author

Robust coherent phonon mode at GaP/Si(001) heterointerface.

Journal of physics. Condensed matter : an Institute of Physics journal·2026
Same author

The Potential of Digital Twins for Pediatric Rare Diseases.

CPT: pharmacometrics & systems pharmacology·2026
Same author

From FAIR to CURE: guidelines for computational models of biological systems.

NPJ systems biology and applications·2026
Same author

The 2025 Westlake Autumn Symposium for Al Proteomics and Virtual Cell.

Genomics, proteomics & bioinformatics·2026
Same author

Low Temperature MOCVD Synthesis of High-Mobility 2D InSe.

Small (Weinheim an der Bergstrasse, Germany)·2026

Related Experiment Video

Updated: Mar 30, 2026

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

1.2K

Testing and Validation of Computational Methods for Mass Spectrometry.

Laurent Gatto1, Kasper D Hansen2,3, Michael R Hoopmann4

  • 1Computational Proteomics Unit and Cambridge Centre for Proteomics, University of Cambridge , Cambridge CB2 1QR, United Kingdom.

Journal of Proteome Research
|November 10, 2015
PubMed
Summary

Computational methods are crucial for analyzing high-throughput mass spectrometry data. Evaluating these methods is challenging but essential for reliable biological findings, with a new data repository aiding comparisons.

More Related Videos

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments
08:40

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments

Published on: January 20, 2022

5.0K
PTR-ToF-MS Coupled with an Automated Sampling System and Tailored Data Analysis for Food Studies: Bioprocess Monitoring, Screening and Nose-space Analysis
08:43

PTR-ToF-MS Coupled with an Automated Sampling System and Tailored Data Analysis for Food Studies: Bioprocess Monitoring, Screening and Nose-space Analysis

Published on: May 11, 2017

13.1K

Related Experiment Videos

Last Updated: Mar 30, 2026

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

1.2K
Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments
08:40

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments

Published on: January 20, 2022

5.0K
PTR-ToF-MS Coupled with an Automated Sampling System and Tailored Data Analysis for Food Studies: Bioprocess Monitoring, Screening and Nose-space Analysis
08:43

PTR-ToF-MS Coupled with an Automated Sampling System and Tailored Data Analysis for Food Studies: Bioprocess Monitoring, Screening and Nose-space Analysis

Published on: May 11, 2017

13.1K

Area of Science:

  • Computational biology
  • Bioinformatics
  • Mass spectrometry data analysis

Background:

  • High-throughput mass spectrometry (e.g., proteomics, metabolomics) generates vast datasets requiring computational analysis.
  • The choice of computational method significantly impacts biological study outcomes, yet method performance is often underappreciated.
  • Unbiased comparison of computational methods is challenging due to data volume and algorithmic complexity.

Purpose of the Study:

  • To discuss challenges in testing and validating computational methods for mass spectrometry data.
  • To explore different data types (simulated and experimental) and metrics for method comparison.
  • To introduce a new public repository for mass spectrometry reference datasets to facilitate performance evaluation.

Main Methods:

  • Discussion of validation strategies for computational methods.
  • Review of data types used in method evaluation (simulated vs. experimental).
  • Introduction of a public repository (http://compms.org/RefData) with reference datasets.

Main Results:

  • Identified challenges in unbiased comparison of computational methods.
  • Highlighted the importance of selecting appropriate validation data and metrics.
  • Launched a public repository to support method performance evaluation.

Conclusions:

  • Rigorous validation of computational methods is critical for accurate biological interpretation.
  • Standardized datasets and evaluation metrics are needed for reliable method comparison.
  • The new repository provides a valuable resource for the scientific community to assess computational tools.