Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Mass Spectrometry: Overview

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: Complex Analysis

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 Spectrum: Interpretation

Mass Spectrum: Interpretation

An unknown compound can be established by identifying the molecular ion peak in the mass spectrum. The molecular ion peak is often weak or absent due to the predominance of fragmentation in high-energy electron beams. In such cases, a soft-energy electron beam can be used to scan the spectrum to enhance the intensity of the molecular ion peak. Additionally, chemical ionization, field ionization, and desorption ionization spectra are used to obtain a relatively intense molecular ion peak.To...

High-Resolution Mass Spectrometry (HRMS)

High-Resolution Mass Spectrometry (HRMS)

The resolution of a mass spectrometer depends on the efficiency of separating ions with different ion masses. The mass of an atom is approximated to the sum of the masses of protons and neutrons inside, considering the masses of protons and neutrons as equal. However, the masses of the proton (1.6726 × 10−24 g) and neutron (1.6749 × 10−24 g) are not truly equal. There is a minor error in the expression of atomic masses relative to the simplest atom of hydrogen. For example, the mass of helium...

MALDI-TOF Mass Spectrometry

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...

You might also read

Related Articles

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

Sort by

Same author

Community-driven advances in computational mass spectrometry: The perspective of EuBIC-MS members.

Journal of proteomics·2026

Same author

The spatial proteome of the Plasmodium falciparum schizont illuminates the composition and evolutionary trajectories of its organelles.

Nature communications·2026

Same author

Association of nasopharyngeal <i>Dolosigranulum pigrum</i> and <i>Corynebacterium</i> species with post-acute sequelae of SARS-CoV-2 in a longitudinal cohort.

Microbiology spectrum·2026

Same author

Dynamic subcellular proteomics identifies regulators of adipocyte insulin action.

Nature communications·2026

Same author

Subcellular localization as a driver of protein function.

Nature reviews. Molecular cell biology·2026

Same author

Functional characterisation of tumour suppressor PDCD4 reveals previously undisclosed role in the control of cell adhesion.

Nucleic acids research·2026

Search research articles

Related Experiment Video

Updated: May 27, 2026

Dissecting Multi-protein Signaling Complexes by Bimolecular Complementation Affinity Purification (BiCAP)

Dissecting Multi-protein Signaling Complexes by Bimolecular Complementation Affinity Purification (BiCAP)

Published on: June 15, 2018

MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and

Laurent Gatto¹, Kathryn S Lilley

¹Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QR, Cambridge, UK. lg390@cam.ac.uk

Bioinformatics (Oxford, England)

|November 25, 2011

Summary

MSnbase is an R/Bioconductor package for analyzing quantitative proteomics data using isobaric tagging. It offers a framework for reproducible research, including data import, quality control, visualization, and statistical analysis integration.

More Related Videos

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Published on: May 15, 2019

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

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

Published on: August 19, 2025

Related Experiment Videos

Last Updated: May 27, 2026

Dissecting Multi-protein Signaling Complexes by Bimolecular Complementation Affinity Purification (BiCAP)

Dissecting Multi-protein Signaling Complexes by Bimolecular Complementation Affinity Purification (BiCAP)

Published on: June 15, 2018

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Published on: May 15, 2019

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

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

Published on: August 19, 2025

Area of Science:

Proteomics
Bioinformatics
Computational Biology

Background:

Quantitative proteomics experiments often utilize isobaric tagging for relative quantification.
Analysis of complex proteomics datasets requires specialized software tools.
The R/Bioconductor ecosystem provides a robust platform for bioinformatics research.

Purpose of the Study:

To introduce MSnbase, an R/Bioconductor package designed for the analysis of quantitative proteomics data.
To provide a comprehensive framework for reproducible proteomics data analysis.
To facilitate the integration of quantitative proteomics data with statistical analysis tools.

Main Methods:

MSnbase is implemented in R and available through Bioconductor.
The package supports raw data import, quality control, and visualization.
It includes functionalities for data processing and quantitation of isobaric tagging proteomics experiments.

Main Results:

MSnbase enables exploratory data analysis for reproducible proteomics research.
The package allows direct integration of quantitative proteomics data.
It leverages Bioconductor's statistical analysis facilities.

Conclusions:

MSnbase provides a valuable tool for researchers analyzing quantitative proteomics data.
The package enhances reproducibility in proteomics data analysis workflows.
It facilitates downstream statistical analysis of proteomics experiments.