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

Instrument-Software Synergy in Proteomics: Systematic Evaluation across Mass Spectrometry Platforms, Search Engines, and Rescoring Methods.

Journal of proteome research·2026
Same author

Community-driven advances in computational mass spectrometry: The perspective of EuBIC-MS members.

Journal of proteomics·2026
Same author

Hierarchy of MS-Based Evidence.

Journal of proteome research·2026
Same author

bio.tools: an expanded web service for research software in the life sciences.

Nucleic acids research·2026
Same author

Open and sustainable AI: challenges, opportunities and the road ahead in the life sciences.

Nature methods·2026
Same author

Tackling vaccine hyporesponsiveness through global collaboration, diverse population studies, and data integration.

The Lancet. Microbe·2025

Related Experiment Video

Updated: Jan 19, 2026

Measurement of Protein Turnover Rates in Senescent and Non-Dividing Cultured Cells with Metabolic Labeling and Mass Spectrometry
08:52

Measurement of Protein Turnover Rates in Senescent and Non-Dividing Cultured Cells with Metabolic Labeling and Mass Spectrometry

Published on: April 6, 2022

4.0K

Retention Time Prediction and Protein Identification.

Alex Henneman1, Magnus Palmblad2

  • 1Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.

Methods in Molecular Biology (Clifton, N.J.)
|September 26, 2019
PubMed
Summary

This study explores using separation data in proteomics for protein identification. Predicting peptide retention times in reversed-phase chromatography aids in bottom-up proteomics validation.

Keywords:
Liquid chromatographyMass spectrometryPeptidePredictionProtein identificationRetention time

More Related Videos

Author Spotlight: Advancing Tear Fluid Analysis Using a Standardized Protocol for Proteomics Research
08:20

Author Spotlight: Advancing Tear Fluid Analysis Using a Standardized Protocol for Proteomics Research

Published on: December 1, 2023

3.1K
A Mass Spectrometry-Based Proteomics Approach for Global and High-Confidence Protein R-Methylation Analysis
09:40

A Mass Spectrometry-Based Proteomics Approach for Global and High-Confidence Protein R-Methylation Analysis

Published on: April 28, 2022

2.9K

Related Experiment Videos

Last Updated: Jan 19, 2026

Measurement of Protein Turnover Rates in Senescent and Non-Dividing Cultured Cells with Metabolic Labeling and Mass Spectrometry
08:52

Measurement of Protein Turnover Rates in Senescent and Non-Dividing Cultured Cells with Metabolic Labeling and Mass Spectrometry

Published on: April 6, 2022

4.0K
Author Spotlight: Advancing Tear Fluid Analysis Using a Standardized Protocol for Proteomics Research
08:20

Author Spotlight: Advancing Tear Fluid Analysis Using a Standardized Protocol for Proteomics Research

Published on: December 1, 2023

3.1K
A Mass Spectrometry-Based Proteomics Approach for Global and High-Confidence Protein R-Methylation Analysis
09:40

A Mass Spectrometry-Based Proteomics Approach for Global and High-Confidence Protein R-Methylation Analysis

Published on: April 28, 2022

2.9K

Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biochemistry

Background:

  • Bottom-up proteomics typically identifies proteins via peptide mass spectrometry.
  • Separation techniques like chromatography fractionate complex mixtures, improving data quality by reducing ion suppression.
  • Separation methods provide physical and chemical property data (e.g., molecular weight, hydrophobicity) that can be predicted from amino acid sequences.

Purpose of the Study:

  • To review the use of separation data for protein identification and validation in proteomics.
  • To emphasize the prediction of tryptic peptide retention times in reversed-phase chromatography for bottom-up proteomics.

Main Methods:

  • Enzymatic digestion of proteins into peptides.
  • Tandem mass spectrometry for peptide analysis.
  • Liquid chromatography and electrophoresis for sample fractionation.
  • Prediction of peptide properties (e.g., retention times) based on amino acid sequences.

Main Results:

  • Separation methods yield data on peptide/protein properties like molecular weight, isoelectric point, charge, and hydrophobicity.
  • These properties can be predicted from amino acid sequences with a degree of accuracy.
  • Focus on predicting retention times in reversed-phase chromatography under acidic conditions.

Conclusions:

  • Data from separation methods can be effectively used for protein identification and validation in proteomics.
  • Predictive models for peptide behavior in chromatography enhance bottom-up proteomics workflows.
  • Reversed-phase chromatography retention time prediction is a key application in modern proteomics.