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

8.8K
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...
8.8K
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

2.8K
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...
2.8K
Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

2.0K
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...
2.0K
Mass Analyzers: Overview01:13

Mass Analyzers: Overview

2.0K
The mass analyzer is a crucial component of the mass spectrometer. In the ionization chamber, the vaporized sample is bombarded with a high-energy electron beam to generate a radical cation and further fragment into neutral molecules, radicals, and cations. A series of negatively charged accelerator plates accelerate the cations into the mass analyzer. The mass analyzer separates ions according to their mass-to-charge (m/z) ratios and then directs them to the detector. The common types of mass...
2.0K
MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

7.4K
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...
7.4K
Mass Spectrum: Interpretation01:24

Mass Spectrum: Interpretation

3.8K
An unknown compound can be established by identifying the molecular ion peak in the mass spectrum. The molecular ion peak is often weak or absent due to the predominance of fragmentation in high-energy electron beams. In such cases, a soft-energy electron beam can be used to scan the spectrum to enhance the intensity of the molecular ion peak. Additionally, chemical ionization, field ionization, and desorption ionization spectra are used to obtain a relatively intense molecular ion peak.To...
3.8K

You might also read

Related Articles

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

Sort by
Same author

AI-driven discovery of GPNMB CAR T cells as a multi-cancer therapy.

Cell·2026
Same author

<i>Proteomes</i> Annual Report Card 2025.

Proteomes·2026
Same author

CAR-T cells targeting fibroblast activation protein eliminate pathological fibroblasts and preserve cardiac function in a Duchenne Muscular Dystrophy murine model.

Stem cell research & therapy·2026
Same author

Hopx(+) optic nerve head-astrocytes counter neuronal stress and glaucoma damage.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Urine Proteomics Identifies Biomarkers for Diagnosis and Fibrosis Severity in Pediatric Chronic Pancreatitis.

Clinical and translational gastroenterology·2026
Same author

Anti-FAP CAR T cells produced in vivo reduce fibrosis and restore liver homeostasis in metabolic dysfunction-associated steatohepatitis.

Science translational medicine·2026
Same journal

Light-Induced Proteomic Changes in Pseudomonas aeruginosa Biofilms.

Proteomics·2026
Same journal

Decade-Resolved Proteomic Profiling of Gastric Cancer FFPE Archives: Evaluating Storage-Associated Shifts and Signal Stability Over 50 Years.

Proteomics·2026
Same journal

Proteome-Scale Mining of Metal-Associated Proteins of Monkeypox Virus.

Proteomics·2026
Same journal

Optimized Sample Handling Minimizes Peptide Adsorption to Plastics to Enable High Sensitivity Evosep Based Chemical Proteomics.

Proteomics·2026
Same journal

Toward Predicting Pandemic Potential: A Comparative Analysis of Virus-Host Interactions Between Diverse Influenza A Viruses and the Human Innate Immune System.

Proteomics·2026
Same journal

Functional Divergence of Mucus in Pacific Oyster (Crassostrea gigas): Insights From Integrated Proteomic and Rheological Study.

Proteomics·2026
See all related articles

Related Experiment Video

Updated: Mar 16, 2026

Analyzing Large Protein Complexes by Structural Mass Spectrometry
15:35

Analyzing Large Protein Complexes by Structural Mass Spectrometry

Published on: June 19, 2010

25.0K

ProteinProcessor: A probabilistic analysis using mass accuracy and the MS spectrum.

Jonathan A Epstein1, Paul S Blank2, Brian C Searle3

  • 1Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.

Proteomics
|August 23, 2016
PubMed
Summary
This summary is machine-generated.

This study introduces ProteinProcessor, a new method for protein identification using peptide masses and their errors from MS1 spectra. This tool enhances confidence in protein identifications, especially for those with moderate MS/MS scores.

Keywords:
Bayesian analysisBioinformaticsMALDIProtein sequencingTandem 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

1.2K
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

12.8K

Related Experiment Videos

Last Updated: Mar 16, 2026

Analyzing Large Protein Complexes by Structural Mass Spectrometry
15:35

Analyzing Large Protein Complexes by Structural Mass Spectrometry

Published on: June 19, 2010

25.0K
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

1.2K
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

12.8K

Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • Protein identification commonly relies on tandem mass spectrometry (MS/MS) database searching.
  • Existing methods often overlook valuable information present in MS1-level spectral data.
  • There is a need for enhanced validation of protein identifications, particularly those with moderate confidence scores.

Purpose of the Study:

  • To develop a novel method for confirming protein identifications using MS1 spectral data.
  • To leverage peptide mass measurement errors for a more robust protein identification strategy.
  • To improve the reliability of protein identification in proteomic analyses.

Main Methods:

  • Developed a probability model based on the distribution of mass errors of peptide matches in MS1 spectra.
  • Utilized peptide masses from both fragmented precursor ions and those identified by accurate mass alone.
  • Integrated MS1-level data analysis with existing MS/MS database search results.
  • The method is implemented in a tool named "ProteinProcessor" for MALDI TOF-TOF instrumentation.

Main Results:

  • The ProteinProcessor method provides independent corroboration for protein identifications.
  • It significantly enhances the confirmation of protein identifications, even those with initially moderate MS/MS scores.
  • The approach effectively utilizes previously ignored MS1 spectral data to improve identification accuracy.

Conclusions:

  • The ProteinProcessor tool offers a robust and valuable addition to current protein identification workflows.
  • This method increases confidence in proteomic data by validating identifications using complementary MS1 information.
  • The straightforward application of ProteinProcessor facilitates its integration into routine proteomic analyses.