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

You might also read

Related Articles

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

Sort by
Same author

Global and regional DNA methylation patterns in heart failure: a case-control analysis.

EBioMedicine·2026
Same author

p1/s1, a 3'-nucleotidase/nuclease, allows Leishmania major to circumvent host innate immune response mechanisms.

PLoS pathogens·2026
Same author

Proteomic profiles in inclusion body myositis and polymyositis with mitochondrial pathology.

Acta neuropathologica communications·2026
Same author

Metabolic Profiling of the EmDia Cohort by LC-MS Reveals Empagliflozin-Intake Associated Regulation of 1,5-anhydroglucitol and Urate.

Proteomics·2025
Same author

Employing RNA editing to engineer personalized tumor-specific neoantigens (editopes).

bioRxiv : the preprint server for biology·2025
Same author

Proteome dynamics of chilli pepper fruits during development and ripening from two Mexican cultivars of Capsicum annuum L.

Journal of proteomics·2025
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 8, 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

759

Benchmarking Software for DDA-PASEF Immunopeptidomics.

Yannic Chen1, Annica Preikschat2, Annette Arnold3

  • 1Helmholtz Institute for Translational Oncology Mainz (HI-TRON Mainz) - A Helmholtz Institute of the DKFZ, Mainz, Germany; Division D191 Immunoproteomics Unit, DKFZ German Cancer Research Center, Heidelberg, Germany.

Molecular & Cellular Proteomics : MCP
|December 21, 2025
PubMed
Summary
This summary is machine-generated.

This study benchmarks immunopeptidomics software, finding PEAKS and FragPipe identify the most immunopeptides. Database size impacts performance, highlighting the need for careful software selection in mass spectrometry analysis.

Keywords:
DDA-PASEFHLA-bound peptidesdatabase searchimmunopeptidomicssoftware tools benchmark

More Related Videos

Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

515
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

7.2K

Related Experiment Videos

Last Updated: Jan 8, 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

759
Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

515
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

7.2K

Area of Science:

  • Immunopeptidomics
  • Mass Spectrometry (MS)
  • Proteomics

Background:

  • Mass spectrometry is crucial for high-throughput immunopeptide identification.
  • Immunopeptide identification requires sophisticated algorithms due to a lack of proteolytic specificity.
  • A systematic evaluation of immunopeptidomics data processing software is lacking.

Purpose of the Study:

  • To comprehensively benchmark widely used data-dependent acquisition (DDA)-based software for immunopeptidomics.
  • To compare the performance, identification confidence, and potential biases of MaxQuant, FragPipe, PEAKS, and MHCquant.
  • To assess the impact of database size on immunopeptide identification efficiency.

Main Methods:

  • Benchmarking of MaxQuant, FragPipe, PEAKS, and MHCquant using Thunder-DDA-PASEF data from the JY cell line.
  • Evaluation of immunopeptide identification capabilities and confidence levels.
  • Analysis of potential biases and the effect of database size on identification.

Main Results:

  • All evaluated software platforms successfully identified prominent immunopeptides with 1% FDR control and medium to high confidence.
  • PEAKS identified the highest number of immunopeptides, followed closely by FragPipe, a strong non-commercial option.
  • Larger database sizes had a variable negative impact on the performance of different software platforms.

Conclusions:

  • The study provides valuable insights into the strengths and limitations of current MS data processing tools for immunopeptidomics.
  • PEAKS and FragPipe are recommended for immunopeptide identification, with FragPipe serving as a viable alternative.
  • The findings aid the immunopeptidomics community in selecting appropriate software for mass spectrometry data analysis.