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

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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...
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

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...
MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

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...
Mass Spectrometry: Overview01:19

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 Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can occur at...
Mass Spectrometry: Complex Analysis01:21

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...

You might also read

Related Articles

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

Sort by
Same author

MLMarker: a machine learning framework for tissue inference and biomarker discovery.

Genome biology·2026
Same author

iDeepLC: Chemical Structure Information Yields Improved Retention Time Prediction of Peptides with Unseen Modifications.

Analytical chemistry·2026
Same author

Harnessing genomic and bioinformatics for surveillance of pathogens in Africa: a scoping review of existing training and gaps in training.

BMC infectious diseases·2026
Same author

Project ODIN: advancing environmental genomic surveillance for public health across sub-Saharan Africa.

The Lancet. Microbe·2026
Same author

omicsGMF: a multi-tool for dimensionality reduction, batch correction and imputation in bulk- and single-cell proteomics.

Nature communications·2026
Same author

The Peptonizer2000: Bringing Confidence to Metaproteomics.

Journal of proteome research·2026
Same journal

Isolation of Mesenchymal Stem Cell-Derived Extracellular Vesicles.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Modeling Melanoma Immune Surveillance by CAR-T Cells in Human Skin Organoids.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Stepwise Optimization of a Matrigel-Based In Vitro Angiogenesis Assay for Reproducible and Quantifiable 2D-Tube Formation Using HUVECs.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Quantifying Mechanical Properties of Fresh Ovarian Tissue with Optical Brillouin Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

3D Chromatin Architecture During Early Development: New Methods and New Findings.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Metabolic Plasticity in Embryogenesis Throughout the Lens of NAD<sup></sup>.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Jun 3, 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

Data management in mass spectrometry-based proteomics.

Lennart Martens1

  • 1Department of Medical Protein Science, Universiteit Gent - VIB, B-9000 Gent, Belgium. lennart.martens@UGent.be

Methods in Molecular Biology (Clifton, N.J.)
|April 7, 2011
PubMed
Summary
This summary is machine-generated.

Mass spectrometry-based proteomics now analyzes thousands of proteins thanks to new methods, instruments, databases, and software. Automating data processing is crucial for managing the high volume of data generated by modern proteomics experiments.

More Related Videos

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions
09:00

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

Published on: April 18, 2025

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
14:51

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

Related Experiment Videos

Last Updated: Jun 3, 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

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions
09:00

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

Published on: April 18, 2025

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
14:51

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

Area of Science:

  • Proteomics
  • Bioinformatics
  • Analytical Chemistry

Background:

  • Mass spectrometry-based proteomics has advanced from analyzing few proteins to high-throughput analysis of thousands.
  • This advancement is driven by innovative methodologies, improved instruments, comprehensive databases, and sophisticated software algorithms.

Purpose of the Study:

  • To provide insight into the bioinformatics challenges of high-throughput proteomics data processing.
  • To outline a typical data processing workflow, data types, and user roles.
  • To discuss available software solutions and data management strategies.

Main Methods:

  • Review of mass spectrometry-based proteomics workflows.
  • Analysis of data types and user roles in proteomics data processing.
  • Overview of software solutions for proteomics data analysis and management.

Main Results:

  • High-throughput proteomics generates a substantial bioinformatics challenge due to the volume of data.
  • Automation of data processing workflows is essential for managing modern proteomics data.
  • Effective data management and dissemination are critical for global proteomics research.

Conclusions:

  • The transition to high-throughput proteomics necessitates robust data management and automated processing.
  • Sophisticated software and comprehensive databases are key enablers of modern proteomics.
  • Integrating local data management with global dissemination is vital for advancing proteomics research.