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

Insensitive Nuclei Enhanced by Polarization Transfer (INEPT)01:15

Insensitive Nuclei Enhanced by Polarization Transfer (INEPT)

453
Insensitive Nuclei Enhanced by Polarization Transfer (INEPT) is an advanced Nuclear Magnetic Resonance (NMR) technique specifically designed to detect and enhance the signals of low-abundance nuclei, such as carbon-13 and nitrogen-15, in small molecules. The fundamental principle behind INEPT is the transfer of polarization from a more abundant and highly polarizable nucleus, typically hydrogen-1, to the low-abundance nucleus of interest. This process effectively boosts the NMR signal of the...
453
¹³C NMR: ¹H–¹³C Decoupling01:04

¹³C NMR: ¹H–¹³C Decoupling

1.2K
The probability of having two carbon-13 atoms next to each other is negligible because of the low natural abundance of carbon-13. Consequently, peak splitting due to carbon-carbon spin-spin coupling is not observed in spectra. However, protons up to three sigma bonds away split the carbon signal according to the n+1 rule, resulting in complicated spectra.
A broadband decoupling technique is used to simplify these complex, sometimes overlapping, signals. Broadband decoupling relies on a...
1.2K
¹H NMR: Complex Splitting01:13

¹H NMR: Complex Splitting

1.3K
A proton M that is coupled to a proton X results in doublet signals for M. However, NMR-active nuclei can be simultaneously coupled to more than one nonequivalent nucleus. When M is coupled to a second proton A, such as in styrene oxide, each peak in the doublet is split into another doublet.
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied...
1.3K
Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

3.5K
The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can...
3.5K
¹H NMR: Interpreting Distorted and Overlapping Signals01:02

¹H NMR: Interpreting Distorted and Overlapping Signals

1.1K
Spin systems where the difference in chemical shifts of the coupled nuclei is greater than ten times J are called first-order spin systems. These nuclei are weakly coupled, and their chemical shifts and coupling constant can generally be estimated from the well-separated signals in the spectrum.
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are...
1.1K
Mass Analyzers: Overview01:13

Mass Analyzers: Overview

774
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...
774

You might also read

Related Articles

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

Sort by
Same author

Corona: A Virtual Mass Spectrometer for the Development of Real-Time Mass Spectrometry Software.

Analytical chemistry·2026
Same author

A unified photosensitizer platform for <i>in situ</i> DNA-, RNA-, and protein-directed proximity labeling.

bioRxiv : the preprint server for biology·2026
Same author

Spatial atlas of diabetic kidney disease reveals a B cell-rich subgroup.

Nature·2026
Same author

The proteomic landscape and temporal dynamics of human and mouse gastruloid development.

Nature cell biology·2026
Same author

Serum proteomics reveals distinct phenotypic signatures to IL-6 blockade between two immunotherapies.

bioRxiv : the preprint server for biology·2026
Same author

DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci.

eLife·2026

Related Experiment Video

Updated: Aug 20, 2025

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode
09:19

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

Published on: June 4, 2021

3.4K

Conditional Fragment Ion Probabilities Improve Database Searching for Nonmonoisotopic Precursors.

Jonathon J O'Brien1, Meagan Gadzuk-Shea2, Phillip M Seitzer1

  • 1Calico Laboratories, South San Francisco, California94080, United States.

Journal of Proteome Research
|November 22, 2022
PubMed
Summary

This study introduces Comet-CIDS, a new proteomics search algorithm that improves peptide and protein identification rates. By accounting for isotopic variability in labeled peptides, it enhances accuracy in mass spectrometry data analysis.

Keywords:
D2Odatabase searchingisotopic envelope 15Npeptide spectrum matchingprotein turnoverstable isotope labeling

More Related Videos

Enhanced Sample Multiplexing of Tissues Using Combined Precursor Isotopic Labeling and Isobaric Tagging cPILOT
09:06

Enhanced Sample Multiplexing of Tissues Using Combined Precursor Isotopic Labeling and Isobaric Tagging cPILOT

Published on: May 1, 2017

7.0K
Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery
06:26

Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery

Published on: May 16, 2021

4.9K

Related Experiment Videos

Last Updated: Aug 20, 2025

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode
09:19

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

Published on: June 4, 2021

3.4K
Enhanced Sample Multiplexing of Tissues Using Combined Precursor Isotopic Labeling and Isobaric Tagging cPILOT
09:06

Enhanced Sample Multiplexing of Tissues Using Combined Precursor Isotopic Labeling and Isobaric Tagging cPILOT

Published on: May 1, 2017

7.0K
Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery
06:26

Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery

Published on: May 16, 2021

4.9K

Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Computational Biology

Background:

  • Stochastic precursor ion isolation in mass spectrometry can lead to isotopically enriched fragment ions.
  • This issue is significant in large peptide analysis and stable isotope labeling (SIL) experiments (e.g., deuterium or 15N labeling).
  • Incomplete or ubiquitous labeling generates peptide ions with multiple structural isomers, complicating analysis.

Purpose of the Study:

  • To address the limitations of current proteomics search algorithms in handling isotopic variability.
  • To improve peptide and protein identification rates in SIL experiments.
  • To develop a method that accurately predicts isotopic distributions of fragment ions.

Main Methods:

  • Derived expected isotopic distributions for each fragment ion.
  • Integrated these distributions into theoretical mass spectra for peptide-spectrum matching.
  • Adapted the Comet search platform to incorporate a modified spectral prediction algorithm named Conditional fragment Ion Distribution Search (CIDS).
  • Comet-CIDS computes isotopic distributions for each candidate peptide's fragments to match observed m/z distributions.

Main Results:

  • Comet-CIDS identified more confident peptide-spectrum matches compared to traditional methods.
  • Achieved higher protein sequence coverage in evaluated D2O and 15N labeled datasets.
  • The improvement in identification rates correlated with the extent of isotopic labeling in the sample.

Conclusions:

  • The Conditional fragment Ion Distribution Search (CIDS) algorithm enhances the accuracy of peptide and protein identification in proteomics.
  • Accounting for isotopic variability is crucial for improving search algorithm performance, especially in stable isotope labeling studies.
  • Comet-CIDS offers a more robust approach for analyzing complex mass spectrometry data from labeled proteomic samples.