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

8.1K
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...
8.1K
Proteomics01:33

Proteomics

9.4K
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...
9.4K

You might also read

Related Articles

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

Sort by
Same author

Translational insights into extracellular vesicles in peritoneal dialysis.

Peritoneal dialysis international : journal of the International Society for Peritoneal Dialysis·2026
Same author

Integrating multi-omics data for next-generation cancer research and precision medicine.

Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico·2026
Same author

Co-research in the development of AI and digital health tools for cancer management and care: a systematic review.

BMC health services research·2026
Same author

Proteomics of human duodenum in pre-diabetes and type 2 diabetes reveals potential novel therapeutic targets for aetiology and therapeutics.

Clinical proteomics·2026
Same author

Ethical and clinical challenges in managing low-penetrance CNVs: insights from Portuguese clinical geneticists.

Frontiers in genetics·2026
Same author

Metabolic reprogramming regulates histone lactylation during zebrafish caudal fin regeneration.

iScience·2026
Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Jan 19, 2026

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

12.6K

Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry.

Rune Matthiesen1, Ana Sofia Carvalho2

  • 1Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal.

Methods in Molecular Biology (Clifton, N.J.)
|September 26, 2019
PubMed
Summary
This summary is machine-generated.

This study overviews common mass spectrometry methods and algorithms for protein quantitation in proteomics. It highlights using R packages to build customizable pipelines for reliable protein and peptide data analysis.

Keywords:
Label-free quantitationLiquid chromatographyMass spectrometryPeptide quantitationProtein quantitationStable isotope labeling

More Related Videos

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification
09:04

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Published on: August 17, 2015

17.5K
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

6.1K

Related Experiment Videos

Last Updated: Jan 19, 2026

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

12.6K
Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification
09:04

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Published on: August 17, 2015

17.5K
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

6.1K

Area of Science:

  • Proteomics
  • Biochemistry
  • Computational Biology

Background:

  • Mass spectrometry (MS) is crucial for protein discovery and clinical proteomics, offering protein identification, quantitation, and post-translational modification analysis.
  • Protein array technologies are limited to targeted protein and modification quantitation, unlike the comprehensive data from MS.
  • Numerous quantitative MS methods exist, necessitating clear guidance for reliable data interpretation.

Purpose of the Study:

  • To provide an overview of common mass spectrometry (MS) methods and algorithms for quantitative proteomics.
  • To discuss computational aspects essential for obtaining reliable quantitative measures of proteins, peptides, and post-translational modifications.
  • To explore the development of customizable data analysis pipelines using the R statistical programming language.

Main Methods:

  • Review of prevalent mass spectrometry techniques and associated quantification algorithms.
  • Discussion of computational strategies for processing and analyzing quantitative proteomics data.
  • Exploration of R statistical programming language and its packages for building data analysis pipelines.

Main Results:

  • Identified common mass spectrometry methods and algorithms for protein and peptide quantitation.
  • Discussed computational challenges and solutions for reliable quantitative proteomics data.
  • Demonstrated the potential of R packages for creating customizable quantitative proteomics pipelines.

Conclusions:

  • Mass spectrometry is a powerful tool for comprehensive protein quantitation and PTM analysis in proteomics.
  • Developing robust computational pipelines, particularly using R, is key to reliable quantitative proteomics data analysis.
  • Customizable R-based pipelines offer flexibility and power for diverse quantitative proteomics projects.