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

9.1K
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...
9.1K
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

7.9K
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...
7.9K

You might also read

Related Articles

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

Sort by
Same author

The Local Anesthetic Bupivacaine Inhibits the Progression of Non-Small Cell Lung Cancer by Inducing Autophagy Through Akt/mTOR Signaling.

Frontiers in oncology·2021
Same author

Light exposure mediates circadian rhythms of rhizosphere microbial communities.

The ISME journal·2021
Same author

Novel Potent Selective Orally Active S1P5 Receptor Antagonists.

ACS medicinal chemistry letters·2021
Same author

Biodegradable metals for bone fracture repair in animal models: a systematic review.

Regenerative biomaterials·2021
Same author

Rectangular multilayer dielectric gratings with broadband high diffraction efficiency and enhanced laser damage resistance.

Optics express·2021
Same author

Invariant Image Representation Using Novel Fractional-Order Polar Harmonic Fourier Moments.

Sensors (Basel, Switzerland)·2021
Same journal

Proteomic Profiling of Endothelial Cells Under Laminar Shear Stress Confirms the Importance of KLF4 in the Regulation of Membrane Protein Expression Compared to Oscillatory Flow.

Journal of proteome research·2026
Same journal

Identification of Age-Associated Circulating Proteins and Lipids in 3800 Comorbidity-Enriched Older Adults from Japan-Based Cohorts Using Olink Assays and MRM Mass Spectrometry.

Journal of proteome research·2026
Same journal

Molecular Solution to the Paradox of Ancient Brain Preservation.

Journal of proteome research·2026
Same journal

From Method-Defined Signals to Reference Measurement Procedures: Two Decades of Mass Spectrometry-Based ProGRP Quantification.

Journal of proteome research·2026
Same journal

Proteomic Profiling of Extracellular Vesicle-Enriched Plasma Using Mag-Net for Biomarker Discovery in Pancreatic Ductal Adenocarcinoma.

Journal of proteome research·2026
Same journal

Computationally Efficient Bayesian Estimation of Graphical Networks for Omics Data.

Journal of proteome research·2026
See all related articles

Related Experiment Video

Updated: Dec 18, 2025

Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry
12:49

Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry

Published on: April 4, 2018

12.0K

Data Dependent-Independent Acquisition (DDIA) Proteomics.

Shenheng Guan1,2, Paul P Taylor3, Ziwei Han1

  • 1David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.

Journal of Proteome Research
|June 17, 2020
PubMed
Summary
This summary is machine-generated.

We introduce data dependent-independent acquisition proteomics (DDIA), a novel strategy combining data dependent acquisition and data independent acquisition methods in a single run. DDIA enhances protein identification in proteomics by leveraging DDA data to improve DIA scan analysis.

Keywords:
data-dependent acquisitiondata-independent acquisitiondeep learningpeptide identificationprotein identificationretention time predictionspectrum prediction

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

639
Proteomic Profile of EPS-Urine through FASP Digestion and Data-Independent Analysis
14:48

Proteomic Profile of EPS-Urine through FASP Digestion and Data-Independent Analysis

Published on: May 8, 2021

7.5K

Related Experiment Videos

Last Updated: Dec 18, 2025

Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry
12:49

Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry

Published on: April 4, 2018

12.0K
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

639
Proteomic Profile of EPS-Urine through FASP Digestion and Data-Independent Analysis
14:48

Proteomic Profile of EPS-Urine through FASP Digestion and Data-Independent Analysis

Published on: May 8, 2021

7.5K

Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biochemistry

Background:

  • Data dependent acquisition (DDA) and data independent acquisition (DIA) are distinct, widely used proteomics techniques.
  • Integrating DDA and DIA could potentially enhance proteome coverage and data quality.

Purpose of the Study:

  • To develop and validate a novel strategy combining DDA and DIA into a single LC-MS/MS run.
  • To improve protein and peptide identification in bottom-up proteomics.

Main Methods:

  • Developed a data dependent-independent acquisition (DDIA) strategy for LC-MS/MS.
  • Utilized deep learning-based LC-MS/MS property prediction tools to generate spectral libraries.
  • Implemented a DDIA data processing pipeline with modules for calibration, classifier training, and FDR control.

Main Results:

  • The DDIA method identified a similar number of peptides compared to DIA-Umpire.
  • DDIA achieved nearly twice the number of protein group identifications compared to DIA-Umpire.
  • The DDIA strategy requires minimal input information for data processing.

Conclusions:

  • DDIA offers a powerful integrated approach to bottom-up proteomics.
  • This method enhances protein identification efficiency and requires less prior knowledge for analysis.
  • DDIA represents a significant advancement in proteomics experimental design and data analysis.