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

Proteomics01:33

Proteomics

8.5K
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...
8.5K
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

7.3K
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...
7.3K
Mass Spectrometry of Amines01:19

Mass Spectrometry of Amines

4.7K
In mass spectroscopy, amines undergo fragmentation to give parent ions with odd molecule weights. This observed mass spectrum follows the nitrogen rule: a molecule with an odd number of nitrogen atoms produces a parent ion with an odd molecular weight. The remaining fragments have an even mass.
Amines undergo fragmentation through α cleavage, producing nitrogen-containing cations—iminium ions—and alkyl radicals. Mass spectra of aromatic and cyclic aliphatic amines exhibit...
4.7K

You might also read

Related Articles

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

Sort by
Same author

Comparative genomic analysis of clinically relevant human skin-associated fungi.

Nature communications·2026
Same author

Proteomics reveals spatial and molecular heterogeneities in advanced atherosclerotic carotid artery plaques.

Nature cardiovascular research·2026
Same author

Author Correction: Regulatory T cells in the mouse hypothalamus control immune activation and ameliorate metabolic impairments in high-calorie environments.

Nature communications·2026
Same author

Cysteine availability tunes ubiquitin signaling via inverse stability of LRRC58 E3 ligase and its substrate CDO1.

Nature communications·2026
Same author

Deeper is not always better in plasma proteomics.

Nature biotechnology·2026
Same author

AI-Powered Deep Visual Proteomics Reveals Critical Molecular Transitions in Pancreatic Cancer Precursors.

Cancer discovery·2026
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
Same journal

EDEL: Enhancing Dense Retrievers for Curation of Biomedical Knowledge Bases.

Bioinformatics (Oxford, England)·2026
Same journal

Informative Relational Learning for Adverse Reaction Prediction with Enhanced Generalization to Novel Drugs.

Bioinformatics (Oxford, England)·2026
Same journal

An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.

Bioinformatics (Oxford, England)·2026
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Oct 18, 2025

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

9.4K

AlphaMap: an open-source Python package for the visual annotation of proteomics data with sequence-specific

Eugenia Voytik1, Isabell Bludau1, Sander Willems1

  • 1Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.

Bioinformatics (Oxford, England)
|September 29, 2021
PubMed
Summary
This summary is machine-generated.

AlphaMap is a new Python package for visualizing peptide-level proteomics data. It integrates experimental findings with protein sequence annotations, aiding in the exploration of post-translational modifications and cleavage sites.

More Related Videos

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

3.4K
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

12.9K

Related Experiment Videos

Last Updated: Oct 18, 2025

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

9.4K
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

3.4K
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

12.9K

Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Integrating experimental proteomic data with existing sequence annotations is challenging.
  • A lack of automated analysis platforms hinders the exploration of peptide-level proteomics data.

Purpose of the Study:

  • To present AlphaMap, a Python package for the visual exploration of peptide-level proteomics data.
  • To facilitate the integration of experimental proteomic findings with public sequence annotations.

Main Methods:

  • AlphaMap maps identified peptides and post-translational modifications to protein sequences.
  • It visualizes this data alongside UniProt knowledge and predicted proteolytic cleavage sites.
  • The package offers both a graphical user interface and a Python API for flexible integration.

Main Results:

  • AlphaMap enables visual exploration of peptide-level proteomics data.
  • It integrates experimental data with sequence annotations and prior biological knowledge.
  • The tool generates publication-quality, customizable visualizations.

Conclusions:

  • AlphaMap provides an automated analysis platform for proteomic studies.
  • It enhances the integration and visualization of complex proteomic datasets.
  • The package supports data visualization in common analysis workflows.