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

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...
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...
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...
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: 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...
Mass Spectrometers01:16

Mass Spectrometers

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:

You might also read

Related Articles

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

Sort by
Same author

Interacting Species Database (ISDB): Comprehensive Resource for Interspecies Interactions at the Molecular Level.

Bioinformatics (Oxford, England)·2026
Same author

Meet NUM-ENRICH: A Collaborative National Effort to Extend and Harmonize Research Infrastructures Within the German Network University Medicine.

Studies in health technology and informatics·2026
Same author

Enabling Privacy-Preserving Federated Learning in Healthcare: The FLAME Architecture and Policy Framework.

Studies in health technology and informatics·2026
Same author

A Maturity Model for the Enforcement of PETs in Federated Settings.

Studies in health technology and informatics·2026
Same author

Sequence to structure insights into Lassa virus population-level biophysical properties and glycoprotein structure catalogue.

Npj viruses·2026
Same author

Clinical outcome of biomarker-guided therapies in adult neuro-oncology patients: An update from the Tübingen molecular tumor board cohort.

Neuro-oncology advances·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 6, 2026

Laser Microdissection-Based Protocol for the LC-MS/MS Analysis of the Proteomic Profile of Neuromelanin Granules
07:35

Laser Microdissection-Based Protocol for the LC-MS/MS Analysis of the Proteomic Profile of Neuromelanin Granules

Published on: December 16, 2021

OpenMS and TOPP: open source software for LC-MS data analysis.

Andreas Bertsch1, Clemens Gröpl, Knut Reinert

  • 1Division for Simulation of Biological Systems, WSI/ZBIT, Eberhard-Karls-Universität Tübingen, Tübingen, Germany.

Methods in Molecular Biology (Clifton, N.J.)
|November 11, 2010
PubMed
Summary
This summary is machine-generated.

Automated proteomics data analysis is essential due to large datasets from mass spectrometry. OpenMS and TOPP provide accessible software tools and pipelines for efficient, non-programmer analysis of complex proteomics experiments.

More Related Videos

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

Related Experiment Videos

Last Updated: Jun 6, 2026

Laser Microdissection-Based Protocol for the LC-MS/MS Analysis of the Proteomic Profile of Neuromelanin Granules
07:35

Laser Microdissection-Based Protocol for the LC-MS/MS Analysis of the Proteomic Profile of Neuromelanin Granules

Published on: December 16, 2021

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

Area of Science:

  • Proteomics
  • Computational Biology
  • Bioinformatics

Background:

  • Mass spectrometry generates vast proteomics data, overwhelming manual analysis.
  • Need for automated, robust, and reusable software tools for data interpretation.

Purpose of the Study:

  • Introduce OpenMS, a software library for mass spectrometry data analysis.
  • Present TOPP (The OpenMS Proteomics Pipeline) for accessible proteomics data analysis.
  • Enable non-programmers to utilize sophisticated proteomics algorithms.

Main Methods:

  • Development of the OpenMS software library with diverse data structures and algorithms.
  • Implementation of TOPP, a collection of user-friendly tools within OpenMS.
  • Integration of TOPP tools into customizable analysis pipelines.
  • Graphical editor for constructing complex analytical workflows.

Main Results:

  • OpenMS provides a comprehensive set of algorithms for proteomics data.
  • TOPP simplifies access to advanced OpenMS functionalities for non-programmers.
  • Pipelines can be built to automate mass spectrometry data analysis from raw output.
  • Complex workflows are manageable through a graphical interface.

Conclusions:

  • OpenMS and TOPP significantly enhance the accessibility and efficiency of proteomics data analysis.
  • These tools empower researchers, including non-programmers, to conduct sophisticated mass spectrometry experiments.
  • Streamlined analysis pipelines facilitate easier interpretation of complex biological data.