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

Proteomics and human microchips identify Thrombospondin-1 as a potential biomarker for calciphylaxis stem cell therapy.

iScience·2026
Same author

OpenIO: An open framework for AI-native immunotherapy.

Cancer cell·2026
Same author

Spatial distribution of the proteome in the human body and in cancers.

Nature·2026
Same author

MetaTree: an interactive web platform for aligned hierarchical data visualization and multi-group comparison.

BMC bioinformatics·2026
Same author

Individual variability shapes ex vivo responses to resistant starch in inflammatory bowel disease derived microbiomes.

NPJ biofilms and microbiomes·2026
Same author

Allelic variation in UVR8 modulates thermotolerance-yield tradeoffs in plants.

Cell research·2026
Same journal

Tranquillyzer: A Neural Network Framework for Long-read Annotation and Demultiplexing.

Genomics, proteomics & bioinformatics·2026
Same journal

Advancing Functional Transcriptomics in Zebrafish with High-accuracy Full-length RNA Sequencing.

Genomics, proteomics & bioinformatics·2026
Same journal

NanoRAPID: A Deep Learning-based Framework for Single-molecule RNA Structure Analysis Using Nanopore Direct RNA Sequencing.

Genomics, proteomics & bioinformatics·2026
Same journal

Single-cell Multiomic and Spatiotemporal Dissection of the Liver Circadian Clock.

Genomics, proteomics & bioinformatics·2026
Same journal

Ï€-HelixNovo2: Making Accurate Online De Novo Peptide Sequencing Available to All.

Genomics, proteomics & bioinformatics·2026
Same journal

CTSC-RAB38 Potentiates Responsiveness to PD-1 Blockade in Esophageal Squamous Cell Carcinoma.

Genomics, proteomics & bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Apr 7, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

1.1K

MetaDIA: A DDA-free Database Reduction Strategy for DIA Human Gut Metaproteomics.

Haonan Duan1,2, Zhibin Ning2, Zhongzhi Sun2

  • 1Nanjing Women and Children's Healthcare Hospital, Women's Hospital of Nanjing Medical University, Nanjing 210004, China.

Genomics, Proteomics & Bioinformatics
|April 5, 2026
PubMed
Summary
This summary is machine-generated.

This study introduces MetaDIA, a new method for analyzing gut microbiome data. MetaDIA improves the speed and accuracy of identifying peptides in metaproteomics by reducing the search space.

Keywords:
Data independent acquisitionData-dependent acquisition-freeHuman gut microbiomeMetaproteomicsdiaPASEF

More Related Videos

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

1.2K
A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease
09:52

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

Published on: January 10, 2025

1.5K

Related Experiment Videos

Last Updated: Apr 7, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

1.1K
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

1.2K
A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease
09:52

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

Published on: January 10, 2025

1.5K

Area of Science:

  • Microbiology
  • Metaproteomics
  • Bioinformatics

Background:

  • Gut microbiomes are complex, posing challenges for peptide identification in metaproteomics.
  • Current data-independent acquisition (DIA) analysis relies on data-dependent acquisition (DDA) libraries, which are resource-intensive and limiting.

Purpose of the Study:

  • To develop a novel strategy for reducing the search space in metaproteomics.
  • To create an efficient workflow for analyzing DIA microbiome data without DDA assistance.

Main Methods:

  • Utilized species and functional abundance information to score and prioritize peptides.
  • Developed the MetaDIA workflow for DIA metaproteomics data analysis.
  • Created a reduced, sufficient database for DIA data searching.

Main Results:

  • MetaDIA successfully reduced the search space for metaproteomics.
  • The workflow demonstrated strong consistency with traditional DDA-based library approaches.
  • Achieved comparable protein and functional level identifications.

Conclusions:

  • MetaDIA offers an efficient, DDA-independent approach for metaproteomics.
  • This method enhances the application of DIA in microbiome research.
  • MetaDIA is available as an open-source project.