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

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...
High-Resolution Mass Spectrometry (HRMS)01:15

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...
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:
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 Spectrum: Interpretation01:24

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...
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...

You might also read

Related Articles

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

Sort by
Same author

Proteomic profiling of xenobiotic and nutrient transporters in human placenta of different gestational ages.

bioRxiv : the preprint server for biology·2026
Same author

Corona: A Virtual Mass Spectrometer for the Development of Real-Time Mass Spectrometry Software.

Analytical chemistry·2026
Same author

Revisiting resonance-excitation collision-induced dissociation for data-independent acquisition.

bioRxiv : the preprint server for biology·2026
Same author

ToxBase: A Multidimensional ToxCast Reference Database for High-Throughput Human Exposome Analysis.

Environmental science & technology·2026
Same author

Prioritizing peptides for targeted mass spectrometry experiments using deep learning.

bioRxiv : the preprint server for biology·2026
Same author

A quantitative proteomics dataset for assessment and prediction of low dose X-ray radiation exposure in mice.

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: Jun 26, 2026

Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry
12:49

Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry

Published on: April 4, 2018

11.5K

Limelight: An Open, Web-Based Tool for Visualizing, Sharing, and Analyzing Mass Spectrometry Data from DDA Pipelines.

Michael Riffle, Alex Zelter, Daniel Jaschob

  • 1Institute for Systems Biology, Seattle, Washington 98109, United States.

Journal of Proteome Research
|March 4, 2025
PubMed
Summary

Limelight is a new, open-source tool for proteomics data visualization. It enables easy sharing, analysis, and interpretation of data-dependent acquisition (DDA) results from various software pipelines.

Keywords:
DDAdata visualizationmass spectrometryproteomicsserversoftware development

More Related Videos

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
09:29

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

Published on: May 15, 2019

19.3K
Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
12:11

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

6.7K

Related Experiment Videos

Last Updated: Jun 26, 2026

Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry
12:49

Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry

Published on: April 4, 2018

11.5K
Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
09:29

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

Published on: May 15, 2019

19.3K
Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
12:11

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

6.7K

Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • Liquid chromatography-tandem mass spectrometry with data-dependent acquisition (DDA-LC-MS) is a key proteomics technique.
  • Existing DDA data analysis tools often have limited visualization capabilities and are tied to specific software, hindering data sharing and interpretation.
  • This fragmentation restricts the comparison of results across different DDA analysis pipelines.

Purpose of the Study:

  • To develop an accessible, open-source tool for DDA-LC-MS data visualization and sharing.
  • To create a platform independent of specific DDA search software pipelines.
  • To facilitate the interpretation and comparison of proteomics data.

Main Methods:

  • Development of Limelight, a user-friendly, open-source data visualization tool.
  • Implementation of features for accessing and visualizing the entire data stack, from raw scans to identified proteins and modifications.
  • Inclusion of data import tools compatible with various open-mass and closed-mass DDA search engine workflows.

Main Results:

  • Limelight provides a unified platform for DDA-LC-MS data sharing, analysis, and visualization.
  • The tool supports data from diverse DDA workflows and search engines.
  • Users can access and interpret data, including peptide-spectrum matches and protein identifications, using native scores.

Conclusions:

  • Limelight enhances the utility of DDA-LC-MS proteomics data by offering a flexible and collaborative visualization solution.
  • The tool promotes data accessibility and reproducibility in proteomics research.
  • Limelight supports comprehensive data interpretation, from raw spectral data to high-level protein and modification analysis.