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

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

8.1K
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...
8.1K
Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

1.5K
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...
1.5K
Mass Spectrum: Interpretation01:24

Mass Spectrum: Interpretation

2.6K
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...
2.6K
Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation01:01

Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation

2.4K
The fragmentation patterns observed for compounds such as carboxylic acids, esters, and amides in the mass spectra include ⍺-cleavage and McLafferty rearrangement. Fragmentation by ⍺-cleavage preferentially occurs at the carbon-carbon bond at the ⍺-position next to the carboxylic group to generate a neutral radical and a cation. Long chain compounds with hydrogen at their γ-carbon undergo McLafferty rearrangement to give a radical cation and a neutral alkene.
For example, the...
2.4K

You might also read

Related Articles

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

Sort by
Same author

Adenoid-Nasopharyngeal Ratio and craniofacial growth in Children: A two-center longitudinal study with threshold and causal analyses.

European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery·2026
Same author

Crab Shell Inspired Chitin/β-Tricalcium Phosphate Screws as Orthopedic Implants.

Biomacromolecules·2026
Same author

A Preliminary Study of Pig Carcass Decomposition and Necrophagous Fly Community Dynamics on Hainan Island, China.

Insects·2026
Same author

Estimating time of day from fingertip blood samples using RNA molecules with diurnal oscillating expression: a proof-of-principle study.

International journal of legal medicine·2026
Same author

ML-Powered MultiFluid-mRNAplex31: A Self-Developed Panel for Precise Tracing of Five Body Fluids.

Genomics, proteomics & bioinformatics·2026
Same author

An in silico evaluation of tri-allelic SNPs from 1kGP Phase IV data for distant kinship identification and mixture analysis.

Forensic science international. Genetics·2026
Same journal

Biodegradable Self-Powered Electrotherapy Patch for Integrated Smart Wound Management.

Analytical chemistry·2026
Same journal

Metabolite Fraction Libraries for Quantitative NMR Metabolomics.

Analytical chemistry·2026
Same journal

Self-Contained Lateral-Flow Microfluidic Bead-Based Assay for Rapid Quantification of Early-Stage Kidney Biomarkers.

Analytical chemistry·2026
Same journal

Overcoming the Debye Shielding Effect with Concave-Convex Structures for Sensitivity-Enhanced Thin-Film Transistors.

Analytical chemistry·2026
Same journal

Mode-Phase-Difference Photothermal Spectroscopy Assisted by a Bent Biconically Tapered Microfiber for Gas Sensing.

Analytical chemistry·2026
Same journal

Negative-Pressure-Actuated Microfluidics: A Dual-Mode Point-of-Care Sensor for Allergen-Specific IgE in Interstitial Fluid.

Analytical chemistry·2026
See all related articles

Related Experiment Video

Updated: Jan 9, 2026

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics
09:09

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics

Published on: October 13, 2020

5.0K

GPMassSimulator: A Graphormer-Based Method for Glycopeptide MS/MS Spectra Prediction.

Yihui Ren1,2, Dongbo Bu1, Bo Duan3

  • 1Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China.

Analytical Chemistry
|December 9, 2025
PubMed
Summary
This summary is machine-generated.

GPMassSimulator, a deep learning framework, accurately predicts N-glycopeptide spectra and retention times. This advances glycoproteomics by improving the identification of complex glycopeptides, even distinguishing similar structures.

More Related Videos

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides
08:37

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides

Published on: November 2, 2021

2.5K
Glycomics-Guided Glycoproteomics Facilitates Comprehensive Profiling of the Glycoproteome in Complex Tumor Microenvironments
10:59

Glycomics-Guided Glycoproteomics Facilitates Comprehensive Profiling of the Glycoproteome in Complex Tumor Microenvironments

Published on: February 7, 2025

1.7K

Related Experiment Videos

Last Updated: Jan 9, 2026

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics
09:09

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics

Published on: October 13, 2020

5.0K
The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides
08:37

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides

Published on: November 2, 2021

2.5K
Glycomics-Guided Glycoproteomics Facilitates Comprehensive Profiling of the Glycoproteome in Complex Tumor Microenvironments
10:59

Glycomics-Guided Glycoproteomics Facilitates Comprehensive Profiling of the Glycoproteome in Complex Tumor Microenvironments

Published on: February 7, 2025

1.7K

Area of Science:

  • Biochemistry
  • Computational Biology
  • Proteomics

Background:

  • Protein glycosylation is a vital post-translational modification with significant roles in biological processes and disease.
  • Glycoproteomics analysis using mass spectrometry faces challenges due to the structural complexity and heterogeneity of glycopeptides.
  • Current glycopeptide identification tools often underutilize spectral intensity data, limiting their ability to differentiate between similar glycopeptides.

Purpose of the Study:

  • To develop an innovative deep learning framework, GPMassSimulator, for accurate prediction of intact N-glycopeptide tandem mass spectrometry (MS/MS) spectra and retention time.
  • To enhance the discrimination capabilities of glycopeptide identification tools by integrating peptide sequence and glycan structure information.
  • To improve the sensitivity and accuracy of glycopeptide identification in complex biological samples.

Main Methods:

  • Developed GPMassSimulator, a deep learning framework utilizing the GpepFormer module to represent and integrate peptide sequences and glycan structures.
  • Employed a Prediction module within GPMassSimulator to generate theoretical MS/MS spectra and retention times for glycopeptides.
  • Validated the model's performance on a benchmark dataset, including experiments distinguishing similar glycan compositions and isomeric structures.

Main Results:

  • GPMassSimulator achieved 97.1% identification accuracy in distinguishing similar glycan compositions.
  • The framework demonstrated more accurate Top-1 identifications for isomeric structures compared to existing approaches.
  • A rescoring experiment on pGlyco3 data highlighted a significant improvement in the sensitivity of GPMassSimulator for glycopeptide identification.

Conclusions:

  • GPMassSimulator offers a powerful deep learning approach for accurate prediction of N-glycopeptide MS/MS spectra and retention times.
  • The framework effectively captures complex dependencies between peptide sequences and glycan structures, enhancing glycopeptide identification.
  • GPMassSimulator shows significant promise for advancing glycoproteomics research and applications in disease state analysis.