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

7.6K
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...
7.6K
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

6.6K
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...
6.6K

You might also read

Related Articles

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

Sort by
Same author

Fatal emetic Bacillus cereus outbreak associated with consumption of pre-cooked tortellini, Germany, August to September 2024.

International journal of food microbiology·2026
Same author

The State of Peptide Detectability in Computational Proteomics and Guidelines for AI Applications.

Computational and structural biotechnology journal·2026
Same author

Antibiotic Resistance Detection and Concomitant Species Identification of ESKAPE Pathogens by Proteomics.

Molecular & cellular proteomics : MCP·2026
Same author

vPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics.

Nature communications·2025
Same author

New insights into non-contact reflectance IR mapping of teeth.

Faraday discussions·2025
Same author

A MALDI-ToF mass spectrometry database for identification and classification of highly pathogenic bacteria.

Scientific data·2025

Related Experiment Video

Updated: Aug 2, 2025

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
10:37

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

12.0K

Increasing Proteome Depth While Maintaining Quantitative Precision in Short-Gradient Data-Independent Acquisition

Joerg Doellinger1, Christian Blumenscheit1, Andy Schneider1

  • 1Robert Koch-Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin 13353, Germany.

Journal of Proteome Research
|April 18, 2023
PubMed
Summary

Optimizing data-independent acquisition (DIA) for mass spectrometry (MS) with short liquid chromatography (LC) gradients boosts protein identification. Reducing data points per peak (DPPP) enhances proteomic depth and throughput without sacrificing precision.

Keywords:
SPEEDdata points per peakdata-independent acquisitionisolation windowpredicted spectral libraryquantitative proteomics

More Related Videos

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

11.7K
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

6.9K

Related Experiment Videos

Last Updated: Aug 2, 2025

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
10:37

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

12.0K
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

11.7K
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

6.9K

Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Chromatography

Background:

  • Short liquid chromatography (LC) gradients combined with data-independent acquisition (DIA) mass spectrometry (MS) show promise for high-throughput proteomics.
  • Optimization of isolation window schemes, specifically data points per peak (DPPP), is crucial but understudied for DIA-MS.

Purpose of the Study:

  • To investigate the impact of reducing data points per peak (DPPP) on short-gradient DIA-MS.
  • To determine if lower DPPP can enhance protein identification and quantitative precision in high-throughput proteomics.

Main Methods:

  • Employed short LC gradients with DIA-MS.
  • Systematically varied the number of data points per peak (DPPP) in the isolation window scheme.
  • Utilized a Q Exactive HF instrument for analysis.

Main Results:

  • Substantially reducing DPPP in short-gradient DIA-MS significantly increased protein identifications.
  • Quantitative precision was maintained at lower DPPP values.
  • Quantified 6018 HeLa proteins with <20% CV in 30 min, achieving a throughput of 29 samples/day.

Conclusions:

  • Lowering DPPP is a key strategy to maximize proteomic depth and throughput in DIA-MS.
  • The potential for high-throughput DIA-MS applications is currently underestimated.
  • This optimized approach enables deep and precise quantitative proteomics in minimal time.