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

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

6.5K
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...
6.5K

You might also read

Related Articles

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

Sort by
Same author

Absolute quantification of fluorescent protein fusions by mass spectrometry.

Protein science : a publication of the Protein Society·2026
Same author

Publisher Correction: Multiple oestradiol functions inhibit ferroptosis and acute kidney injury.

Nature·2026
Same author

Human assembloids recapitulate periportal liver tissue in vitro.

Nature·2025
Same author

A label-free method for measuring the composition of multicomponent biomolecular condensates.

Nature chemistry·2025
Same author

Publisher Correction: Multiple oestradiol functions inhibit ferroptosis and acute kidney injury.

Nature·2025
Same author

Quantitative imaging of lipid transport in mammalian cells.

Nature·2025

Related Experiment Video

Updated: Jul 5, 2025

Bottom-up and Shotgun Proteomics to Identify a Comprehensive Cochlear Proteome
14:23

Bottom-up and Shotgun Proteomics to Identify a Comprehensive Cochlear Proteome

Published on: March 7, 2014

18.7K

Multispecies Benchmark Analysis for LC-MS/MS Validation and Performance Evaluation in Bottom-Up Proteomics.

Tobias Jumel1, Andrej Shevchenko1

  • 1Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Pfotenhauerstraße 108, 01307 Dresden, Germany.

Journal of Proteome Research
|January 20, 2024
PubMed
Summary

We developed LFQ_bout, a new benchmark tool for validating liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics workflows. This software improves quantification accuracy by identifying and reporting common errors in data processing.

Keywords:
DIA-NNLC-MS/MSaccuracybenchmarkdata-independent acquisition (DIA)differential proteomics analysislabel-free quantification (LFQ)

More Related Videos

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions
09:00

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

Published on: April 18, 2025

604
Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry UPLC-MS
07:34

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry UPLC-MS

Published on: March 14, 2013

12.8K

Related Experiment Videos

Last Updated: Jul 5, 2025

Bottom-up and Shotgun Proteomics to Identify a Comprehensive Cochlear Proteome
14:23

Bottom-up and Shotgun Proteomics to Identify a Comprehensive Cochlear Proteome

Published on: March 7, 2014

18.7K
A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions
09:00

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

Published on: April 18, 2025

604
Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry UPLC-MS
07:34

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry UPLC-MS

Published on: March 14, 2013

12.8K

Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biotechnology

Background:

  • Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is crucial for bottom-up proteomics.
  • Evaluating LC-MS/MS and data processing workflows is essential for accurate proteomic analysis.
  • Current methods for workflow validation can be instrument-dependent and lack standardization.

Purpose of the Study:

  • To introduce an instrument-independent benchmark procedure and software (LFQ_bout) for evaluating bottom-up proteomics workflows.
  • To enable direct comparison of different data processing strategies, including emerging ones like diaPASEF and ScanningSWATH.
  • To assess the impact of undocumented settings and black-box algorithms on quantification accuracy.

Main Methods:

  • Development of the LFQ_bout software for benchmark analysis.
  • Implementation of an instrument-independent procedure for comparative workflow evaluation.
  • Identification and reporting of common quantification errors within LC-MS/MS data processing.

Main Results:

  • The LFQ_bout procedure provides a standardized method for comparing diverse proteomics workflows.
  • The software effectively identifies and quantifies common errors, enhancing data reliability.
  • Performance evaluation of various workflows, including diaPASEF and ScanningSWATH, is facilitated.

Conclusions:

  • LFQ_bout offers a robust solution for validating and comparing LC-MS/MS proteomics workflows.
  • The tool enhances overall performance and quantification accuracy in bottom-up proteomics.
  • Standardized benchmarking improves the reliability and reproducibility of proteomic data analysis.