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

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

20.6K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
20.6K
Peptide Bonds02:43

Peptide Bonds

82.5K
A peptide bond covalently attaches amino acids through a dehydration reaction. One amino acid's carboxyl group and another amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond. The products that such linkages form are peptides. As more amino acids join this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end has the N-terminal, or the amino-terminal, and the other end has a free...
82.5K
Proteomics01:33

Proteomics

9.4K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
9.4K
Predator-Prey Interactions02:39

Predator-Prey Interactions

21.2K
Predators consume prey for energy. Predators that acquire prey and prey that avoid predation both increase their chances of survival and reproduction (i.e., fitness). Routine predator-prey interactions elicit mutual adaptations that improve predator offenses, such as claws, teeth, and speed, as well as prey defenses, including crypsis, aposematism, and mimicry. Thus, predator-prey interactions resemble an evolutionary arms race.
21.2K
Van der Waals Interactions01:24

Van der Waals Interactions

70.9K
Atoms and molecules interact with each other through intermolecular forces. These electrostatic forces arise from attractive or repulsive interactions between particles with permanent, partial, or temporary charges. The intermolecular forces between neutral atoms and molecules are ion–dipole, dipole–dipole, and dispersion forces, collectively known as van der Waals forces.
70.9K
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

8.2K
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...
8.2K

You might also read

Related Articles

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

Sort by
Same author

Systematic optimization and benchmarking of synchro-PASEF for high-throughput phosphoproteome profiling.

bioRxiv : the preprint server for biology·2026
Same author

Morphology Assessment Enabled by Room-Temperature Soft-Landing in Native MS.

International journal of mass spectrometry·2026
Same author

Rapid Peptide Mapping of Monoclonal Antibodies with Direct Infusion Mass Spectrometry.

bioRxiv : the preprint server for biology·2026
Same author

SLX4IP limits replication stress globally and at ALT telomeres.

The EMBO journal·2026
Same author

Discovery urinary metabolomics of preterm neonatal acute kidney injury.

Pediatric nephrology (Berlin, Germany)·2026
Same author

Multi-omic analysis reveals nitric oxide dependent remodeling in classically activated macrophages and identifies negative regulation mediated by AKR1A1.

Redox biology·2026
Same journal

A temporal phospho-acetylome atlas of human myogenesis identifies coordinated post-translational regulation.

Molecular & cellular proteomics : MCP·2026
Same journal

Temporal proteomic characterization of SARS-CoV-2 infected mouse lungs.

Molecular & cellular proteomics : MCP·2026
Same journal

Platelet proteome links metabolism to reactivity in Essential Thrombocythemia.

Molecular & cellular proteomics : MCP·2026
Same journal

Genetic rescue of disrupted synaptic protein interaction network dynamics following SYNGAP1 reactivation.

Molecular & cellular proteomics : MCP·2026
Same journal

ASAP-ID: Proximity labelling with small tags.

Molecular & cellular proteomics : MCP·2026
Same journal

Proteome profiling reveals NQO2 activity contributing to proteasome inhibitor resistance in multiple myeloma cell lines.

Molecular & cellular proteomics : MCP·2026
See all related articles

Related Experiment Video

Updated: Jan 24, 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

912

Interactive Peptide Spectral Annotator: A Versatile Web-based Tool for Proteomic Applications.

Dain R Brademan1, Nicholas M Riley1, Nicholas W Kwiecien1

  • 1Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706; Genome Center of Wisconsin, Madison, WI 53706.

Molecular & Cellular Proteomics : MCP
|May 16, 2019
PubMed
Summary
This summary is machine-generated.

IPSA is a new web tool that visualizes and characterizes peptide tandem mass spectra for researchers. This innovative platform supports various data formats and aids in creating publication-quality figures for scientific studies.

Keywords:
BioinformaticsBioinformatics softwareData evaluationMass SpectrometryPeptides*Quality control and metricsTandem Mass Spectrometry

More Related Videos

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
07:38

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

13.4K
JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

3.6K

Related Experiment Videos

Last Updated: Jan 24, 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

912
Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
07:38

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

13.4K
JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

3.6K

Area of Science:

  • Proteomics
  • Bioinformatics
  • Analytical Chemistry

Background:

  • Peptide tandem mass spectrometry is crucial for protein identification.
  • Visualizing and annotating spectra is essential for data interpretation and quality control.
  • Existing tools may lack flexibility in handling diverse experimental data and output formats.

Purpose of the Study:

  • To introduce IPSA, an innovative web-based spectrum annotator.
  • To provide a versatile tool for visualizing and characterizing peptide tandem mass spectra.
  • To facilitate the creation of publication-quality figures from mass spectrometry data.

Main Methods:

  • Development of a web-based application for spectrum annotation.
  • Support for multiple input data formats including mzTab, mzIdentML, and mzML.
  • Implementation of interactive features for spectrum customization and analysis.
  • Inclusion of support for negative-mode ionization spectra.
  • Export functionality for annotated spectra as editable scalable vector graphics (SVG).

Main Results:

  • IPSA enables visualization and characterization of peptide tandem mass spectra.
  • The tool accommodates a wide range of experimental and instrumental configurations.
  • Customizable annotations and SVG export facilitate figure production.
  • Analysis of single spectra via web forms and batch processing of multiple spectra are supported.
  • Fragment ion statistics can be exported for MS/MS performance characterization.

Conclusions:

  • IPSA is a valuable, freely accessible resource for the proteomics and scientific community.
  • The tool enhances the interpretation and presentation of peptide mass spectrometry data.
  • IPSA supports diverse data inputs and offers flexible output options for publication.
  • The open-source nature of IPSA allows for custom implementations and further development.