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

You might also read

Related Articles

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

Sort by
Same author

Development of a Pharmacogenomics Case Repository for Pharmacy Educators.

American journal of pharmaceutical education·2025
Same author

A Call for Clarity: A Proposed Toolkit to Integrate Foundational Sciences into Pharmacy Curricula.

American journal of pharmaceutical education·2024
Same author

[Impact analysis of atmospheric state for target detection in hyperspectral radiance image].

Guang pu xue yu guang pu fen xi = Guang pu·2012
Same author

[The trend analysis of overweight and obesity in Chinese students during 1985 - 2010].

Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]·2012
Same author

[Analysis of current situation of physical activity and influencing factors in Chinese primary and middle school students in 2010].

Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]·2012
Same author

[Behavioral risk factors for overweight and obesity among Chinese primary and middle school students in 2010].

Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]·2012

Related Experiment Video

Updated: May 9, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

IDPQuantify: combining precursor intensity with spectral counts for protein and peptide quantification.

Yao-Yi Chen1, Matthew C Chambers, Ming Li

  • 1Department of Biomedical Informatics, Vanderbilt University Medical School, Nashville, Tennessee 37232-8575, United States.

Journal of Proteome Research
|July 25, 2013
PubMed
Summary

New software, IDPQuantify, enhances protein quantification in complex samples by combining precursor intensities and spectral counts. This improves the accuracy and sensitivity of differentiating and quantifying protein differences, especially for low-abundance proteins.

More Related Videos

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

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

Related Experiment Videos

Last Updated: May 9, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

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

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

Area of Science:

  • Proteomics
  • Bioinformatics
  • Mass Spectrometry

Background:

  • Label-free quantification in complex proteomic samples faces challenges in sensitivity and specificity.
  • Existing methods using precursor intensities or spectral counts have limitations in accuracy and scope.
  • Precursor intensities offer accurate relative abundance but suffer from missing values; spectral counts are reproducible but limited in quantification.

Purpose of the Study:

  • To develop novel software, IDPQuantify, for enhanced protein differentiation and quantification.
  • To integrate precursor intensities and spectral counts for improved analytical performance.
  • To address limitations in sensitivity and specificity in comparative proteomics.

Main Methods:

  • Developed IDPQuantify software integrating principal component analysis for replicate alignment.
  • Implemented methods to extract accurate precursor intensities from mass spectrometry (MS) data.
  • Combined extracted intensities with spectral counts from IDPicker for robust quantification.

Main Results:

  • IDPQuantify successfully aligned multiple replicates and extracted accurate precursor intensities.
  • The software increased the efficiency of protein quantification, particularly for low-abundance proteins.
  • Combining intensities and spectral counts yielded an average of 30% more true positive differential proteins.

Conclusions:

  • IDPQuantify significantly improves protein differentiation and quantification in complex proteomic samples.
  • The integrated approach enhances sensitivity and specificity compared to traditional methods.
  • The software accurately quantifies protein relative abundance, showing good correlation with known concentrations.