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

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...
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...
MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.Matrix-assisted laser desorption ionization (MALDI) is a commonly...
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called...
Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

Mass spectrometry is an analytical technique used to determine the molecular mass and molecular formula of a compound. The basic principle of mass spectrometry is to generate ions from the analyte molecule and measure these ion abundances against their molecular mass. One common type of ionization, known as electron ionization or EI, bombards the analyte molecules in the gas phase with high-energy electron beams. The electron beams displace an electron from the molecule and leave behind a...
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...

You might also read

Related Articles

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

Sort by
Same author

AURORA A interacts with DICER and SETD2 to promote S-phase progression.

EMBO reports·2026
Same author

Proteome profiling reveals NQO2 activity contributing to proteasome inhibitor resistance in multiple myeloma cell lines.

Molecular & cellular proteomics : MCP·2026
Same author

Pathogenesis of diffuse large B cell lymphoma proteogenotypes.

Cancer cell·2026
Same author

Multi-omics of barley Fusarium Head Blight converge on pathogen-triggered biosynthesis of aromatic amino acid derived chemical defense compounds.

Stress biology·2026
Same author

Rapid photo-crosslinking in living cells reveals protein-nucleic acid dynamics on a timescale of minutes.

Nucleic acids research·2026
Same author

CNS Embryonal Tumour With PLAG Family Gene Alteration: Failure of Response to RET Inhibition.

Neuropathology and applied neurobiology·2026

Related Experiment Video

Updated: May 11, 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

MScDB: a mass spectrometry-centric protein sequence database for proteomics.

Harald Marx1, Simone Lemeer, Susan Klaeger

  • 1Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany.

Journal of Proteome Research
|May 1, 2013
PubMed
Summary
This summary is machine-generated.

A new mass spectrometry-centric protein sequence database (MScDB) was developed. It improves proteomic data analysis by grouping indistinguishable peptides, enhancing protein identification and cross-species research.

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

Capture Compound Mass Spectrometry - A Powerful Tool to Identify Novel c-di-GMP Effector Proteins
12:11

Capture Compound Mass Spectrometry - A Powerful Tool to Identify Novel c-di-GMP Effector Proteins

Published on: March 29, 2015

Related Experiment Videos

Last Updated: May 11, 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

Capture Compound Mass Spectrometry - A Powerful Tool to Identify Novel c-di-GMP Effector Proteins
12:11

Capture Compound Mass Spectrometry - A Powerful Tool to Identify Novel c-di-GMP Effector Proteins

Published on: March 29, 2015

Area of Science:

  • Proteomics
  • Bioinformatics
  • Mass Spectrometry

Background:

  • Protein sequence databases are crucial for life science research, particularly mass spectrometry (MS)-based proteomics.
  • Current databases use sequence similarity clustering, which overlooks the peptide-centric nature of proteomic data and MS capabilities in distinguishing similar sequences.

Purpose of the Study:

  • To introduce a novel approach for structuring protein sequence space at the peptide level.
  • To generate a mass spectrometry-centric protein sequence database (MScDB) that accounts for MS distinguishability of peptides.

Main Methods:

  • Development of MScDB using an in-silico proteolytic digest.
  • Implementation of a peptide-centric clustering algorithm to group indistinguishable protein sequences by MS.
  • Analysis of MScDB against complex human proteomes.

Main Results:

  • Identified 69 peptides not present in UniProtKB and 79 putative single amino acid polymorphisms.
  • MScDB retained ~99% of identifications compared to common databases, with a manageable increase in theoretical peptide search space.
  • Demonstrated cross-species applications, reducing protein assignment uncertainty in human/mouse models to <20%.

Conclusions:

  • MScDB offers a more accurate and efficient protein sequence database for MS-based proteomics.
  • The peptide-centric approach enhances protein identification and enables robust cross-species analyses.
  • This database structure improves the utilization of proteomic data and discovery of novel biological insights.