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

Fast Fourier Transform01:10

Fast Fourier Transform

The Fast Fourier Transform (FFT) is a computational algorithm designed to compute the Discrete Fourier Transform (DFT) efficiently. By breaking down the calculations into smaller, manageable sections, the FFT significantly reduces the computational complexity involved. Direct computation of an N-point DFT requires N2 complex multiplications, whereas the FFT algorithm needs only (N/2)log⁡2N multiplications, offering a much faster performance.
The computational efficiency of the FFT becomes...
Drug Concentration Versus Time Correlation01:15

Drug Concentration Versus Time Correlation

The plasma drug concentration-time curve is a crucial tool in pharmacokinetics, representing the drug's concentration in plasma at different time intervals post-administration. This curve illustrates the drug's journey from absorption into the systemic circulation, distribution to body tissues, and eventual elimination through excretion or biotransformation.
Two pivotal parameters are the minimum effective concentration (MEC) and the minimum toxic concentration (MTC). The MEC is the lowest drug...
Cross Product01:25

Cross Product

The cross product is a fundamental concept in vector algebra that is a vector operation on two different vectors to obtain a third vector. Unlike the scalar product, the cross product results in a vector quantity perpendicular to both the original vectors.
The magnitude of the cross product is obtained by multiplying the magnitude of both the vectors and the sine of the angle between them. This means that a larger angle between the vectors will lead to a greater magnitude of the cross product.
Linear Approximation in Time Domain01:21

Linear Approximation in Time Domain

Nonlinear systems often require sophisticated approaches for accurate modeling and analysis, with state-space representation being particularly effective. This method is especially useful for systems where variables and parameters vary with time or operating conditions, such as in a simple pendulum or a translational mechanical system with nonlinear springs.
For a simple pendulum with a mass evenly distributed along its length and the center of mass located at half the pendulum's length, the...
2D NMR: Overview of Heteronuclear Correlation Techniques01:18

2D NMR: Overview of Heteronuclear Correlation Techniques

Heteronuclear correlation spectroscopy is an analytical technique that investigates the coupling between different types of nuclei, often a proton and an X-nucleus, such as carbon-13 or nitrogen-15. This method is commonly used in nuclear magnetic resonance (NMR) spectroscopy to gain insights into complex chemical compounds' structural and compositional aspects. A typical heteronuclear correlation spectrum displays X-nucleus chemical shifts on one axis and a proton spectrum on the other axis.
Cluster Sampling Method01:20

Cluster Sampling Method

Appropriate sampling methods ensure that samples are drawn without bias and accurately represent the population. Because measuring the entire population in a study is not practical, researchers use samples to represent the population of interest.
To choose a cluster sample, divide the population into clusters (groups) and then randomly select some of the clusters. All the members from these clusters are in the cluster sample. For example, if you randomly sample four departments from your...

You might also read

Related Articles

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

Sort by
Same author

Site Confidence Scores among All Available Structures to Help Infer Conformational Origins of Identified Cross-Links.

Journal of proteome research·2026
Same author

Unravelling proteomic changes of primary bovine endometrial epithelial cells to lipopolysaccharide and lipoteichoic acid bacterial ligand stimulation.

Research in veterinary science·2026
Same author

Molecular Responses to Climate Change: How Warming and Acidification Reshape the Proteome and Phosphoproteome of the Endangered Mira Chub.

Ecology and evolution·2026
Same author

Postoperative Opioid Use Is Uncommon After Third- and Fourth-Generation Percutaneous Hallux Valgus Surgery: A Prospective Single-Surgeon Case Series.

Foot & ankle international·2026
Same author

Proteomic comparison of intact and fetoscopy-induced fetal membrane defect sites.

Pediatric research·2025
Same author

The Montecranon classification-a comprehensive treatment strategy for complex proximal ulna fracture dislocations.

JSES international·2025
Same journal

Proteomic Profiling of Extracellular Vesicle-Enriched Plasma Using Mag-Net for Biomarker Discovery in Pancreatic Ductal Adenocarcinoma.

Journal of proteome research·2026
Same journal

Computationally Efficient Bayesian Estimation of Graphical Networks for Omics Data.

Journal of proteome research·2026
Same journal

Hierarchy of MS-Based Evidence.

Journal of proteome research·2026
Same journal

Proteomic Profiling of Exosomes from HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinoma: Selective Cargo Packaging.

Journal of proteome research·2026
Same journal

Proteomic Analysis Identifies ATE1-Dependent Arginylation Dysregulation across Meningioma Grades.

Journal of proteome research·2026
Same journal

Proteomic Impact of Peripheral Expression of Mutant Huntingtin in <i>C. elegans</i>.

Journal of proteome research·2026
See all related articles

Related Experiment Video

Updated: Jul 2, 2026

Dual-Color Fluorescence Cross-Correlation Spectroscopy to Study Protein-Protein Interaction and Protein Dynamics in Live Cells
14:12

Dual-Color Fluorescence Cross-Correlation Spectroscopy to Study Protein-Protein Interaction and Protein Dynamics in Live Cells

Published on: December 11, 2021

A fast SEQUEST cross correlation algorithm.

Jimmy K Eng1, Bernd Fischer, Jonas Grossmann

  • 1Department of Genome Sciences, University of Washington, Seattle, Washington, USA. engj@u.washington.edu

Journal of Proteome Research
|September 9, 2008
PubMed
Summary
This summary is machine-generated.

A new method significantly speeds up peptide identification in mass spectrometry by optimizing the cross-correlation score calculation. This advance enhances the sensitivity and efficiency of tools like SEQUEST for protein analysis.

More Related Videos

Confocal Microscopy Reveals Cell Surface Receptor Aggregation Through Image Correlation Spectroscopy
06:51

Confocal Microscopy Reveals Cell Surface Receptor Aggregation Through Image Correlation Spectroscopy

Published on: August 2, 2018

A Fluorescence Fluctuation Spectroscopy Assay of Protein-Protein Interactions at Cell-Cell Contacts
08:43

A Fluorescence Fluctuation Spectroscopy Assay of Protein-Protein Interactions at Cell-Cell Contacts

Published on: December 1, 2018

Related Experiment Videos

Last Updated: Jul 2, 2026

Dual-Color Fluorescence Cross-Correlation Spectroscopy to Study Protein-Protein Interaction and Protein Dynamics in Live Cells
14:12

Dual-Color Fluorescence Cross-Correlation Spectroscopy to Study Protein-Protein Interaction and Protein Dynamics in Live Cells

Published on: December 11, 2021

Confocal Microscopy Reveals Cell Surface Receptor Aggregation Through Image Correlation Spectroscopy
06:51

Confocal Microscopy Reveals Cell Surface Receptor Aggregation Through Image Correlation Spectroscopy

Published on: August 2, 2018

A Fluorescence Fluctuation Spectroscopy Assay of Protein-Protein Interactions at Cell-Cell Contacts
08:43

A Fluorescence Fluctuation Spectroscopy Assay of Protein-Protein Interactions at Cell-Cell Contacts

Published on: December 1, 2018

Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • SEQUEST is a widely used tool for peptide sequence assignment in tandem mass spectrometry.
  • Its primary scoring function, cross-correlation, is sensitive but computationally intensive.
  • Current SEQUEST implementation uses a preliminary score to limit cross-correlation calculations.

Purpose of the Study:

  • To develop a faster method for calculating the cross-correlation score.
  • To potentially eliminate the need for a preliminary scoring step in SEQUEST.
  • To enable more accurate significance calculations for peptide identifications.

Main Methods:

  • Developed an alternative method for calculating the cross-correlation score without using Fast Fourier Transforms (FFT).
  • Implemented the new method to enable efficient scoring of all candidate peptides.
  • Utilized the distribution of cross-correlation scores for all candidates to calculate E-values.

Main Results:

  • The new method significantly reduces the computation time for the cross-correlation score.
  • This efficiency allows for the scoring of all candidate peptides, not just a subset.
  • Enables direct E-value calculation based on the full score distribution.

Conclusions:

  • The novel cross-correlation calculation method offers a substantial speed improvement for peptide identification.
  • This approach enhances the SEQUEST algorithm's potential for sensitivity and accuracy.
  • Facilitates more robust statistical validation of peptide-spectrum matches in proteomics research.