Jove
Visualize
Contact Us

Related Concept Videos

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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...
Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
High-Resolution Mass Spectrometry (HRMS)01:15

High-Resolution Mass Spectrometry (HRMS)

The resolution of a mass spectrometer depends on the efficiency of separating ions with different ion masses. The mass of an atom is approximated to the sum of the masses of protons and neutrons inside, considering the masses of protons and neutrons as equal. However, the masses of the proton (1.6726 × 10−24 g) and neutron (1.6749 × 10−24 g) are not truly equal. There is a minor error in the expression of atomic masses relative to the simplest atom of hydrogen. For example, the mass of helium...
Proteomics01:33

Proteomics

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 proteomics...

You might also read

Related Articles

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

Sort by
Same author

Interlaboratory Comparison of a Glucagon and Oxyntomodulin Immuno-LC-MS/MS Assay: Implications for Diabetes Research.

Clinical chemistry·2026
Same author

Translational bottlenecks in blood-based proteomics.

EMBO molecular medicine·2026
Same author

Author Correction: Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics.

Nature communications·2026
Same author

Expanding the human proteome with microproteins and peptideins.

Nature·2026
Same author

An AI-Ready Phosphorylation Meta-Analysis for <i>Saccharomyces cerevisiae</i>.

Journal of proteome research·2026
Same author

A Landscape Analysis of Human SUMOylation.

Molecular & cellular proteomics : MCP·2026
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 Experiment Video

Updated: Jun 23, 2026

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
14:51

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

A HUPO test sample study reveals common problems in mass spectrometry-based proteomics.

Alexander W Bell1, Eric W Deutsch, Catherine E Au

  • 1Department of Anatomy and Cell Biology, McGill University, Montreal, Canada.

Nature Methods
|May 19, 2009
PubMed
Summary
This summary is machine-generated.

Reproducibility in proteomics is challenging. A study found that while most labs detected proteins, errors in data analysis, not sample detection, caused missed identifications in liquid chromatography-mass spectrometry.

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

A Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Platform for Investigating Peptide Biosynthetic Enzymes
11:32

A Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Platform for Investigating Peptide Biosynthetic Enzymes

Published on: May 4, 2020

Related Experiment Videos

Last Updated: Jun 23, 2026

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
14:51

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

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

A Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Platform for Investigating Peptide Biosynthetic Enzymes
11:32

A Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Platform for Investigating Peptide Biosynthetic Enzymes

Published on: May 4, 2020

Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biochemistry

Background:

  • Reproducibility is a critical challenge in mass spectrometry-based proteomics.
  • Incompleteness of peptide sampling can lead to errors and hinder reliable protein identification.

Purpose of the Study:

  • To identify common errors causing irreproducibility in liquid chromatography-mass spectrometry (LC-MS) proteomics.
  • To assess the accuracy of protein and peptide identification across multiple laboratories.

Main Methods:

  • An equimolar test sample of 20 purified human proteins was distributed to 27 laboratories.
  • Each protein contained unique tryptic peptides of 1,250 Da for targeted detection.
  • Raw data from all labs were centrally analyzed for comprehensive identification.

Main Results:

  • Only 7 out of 27 labs initially reported all 20 proteins correctly; only 1 lab reported all specific peptides.
  • Centralized analysis revealed all proteins and most peptides were detected by all labs.
  • Key issues identified were missed identifications (false negatives), contamination, and database matching errors.

Conclusions:

  • Initial reporting errors, not detection failures, are major sources of irreproducibility in proteomics.
  • Improvements in search engines and protein identification databases are crucial for accurate mass spectrometry-based proteomics.
  • Standardized data analysis protocols are needed to enhance the reliability of proteomics studies.