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

Low-Dose Radiation Sensitizes Human Nasal Epithelium to Viral Inflammation despite Preserved Structural Integrity.

International archives of allergy and immunology·2026
Same author

The Relationship Between Magnetic Resonance Diffusion Tensor Imaging Parameters and Muscle Dysfunction in Patients with Osteoporosis: A Cross-Sectional Retrospective Study.

International journal of general medicine·2026
Same author

Integrating network toxicology, machine learning, and experimental evidence reveals candidate targets and pathways in PCDD/F-related colon cancer.

Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association·2026
Same author

Glucagon-like peptide-1 receptor agonists ameliorate polycystic ovarian syndrome in mice by regulating the irisin level and activating the BMP4-Smad signaling pathway†.

Biology of reproduction·2026
Same author

Multiarm single-port robot-assisted secondary carinal reconstruction for right main bronchial schwannoma: A case report.

JTCVS techniques·2026
Same author

An Integrated Approach Combining Surface Plasmon Resonance Screening with Proteomics Enables Discovery of Natural Molecular Glue Degraders.

JACS Au·2026

Related Experiment Video

Updated: Dec 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

12.5K

Normalization Method Utilizing Endogenous Proteins for Quantitative Proteomics.

Kai Yan1, Yueying Yang1, Yunpeng Zhang1

  • 1Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China.

Journal of the American Society for Mass Spectrometry
|April 9, 2020
PubMed
Summary
This summary is machine-generated.

We developed a novel protein normalization method using endogenous protein standards. This technique effectively reduces data bias and improves biomarker discovery for diseases like colorectal cancer.

Keywords:
biomarkerendogenous protein normalizationglobal biasquantitative proteomics

More Related Videos

Robust Comparison of Protein Levels Across Tissues and Throughout Development Using Standardized Quantitative Western Blotting
08:13

Robust Comparison of Protein Levels Across Tissues and Throughout Development Using Standardized Quantitative Western Blotting

Published on: April 9, 2019

14.7K
Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification
09:04

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Published on: August 17, 2015

17.4K

Related Experiment Videos

Last Updated: Dec 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

12.5K
Robust Comparison of Protein Levels Across Tissues and Throughout Development Using Standardized Quantitative Western Blotting
08:13

Robust Comparison of Protein Levels Across Tissues and Throughout Development Using Standardized Quantitative Western Blotting

Published on: April 9, 2019

14.7K
Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification
09:04

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Published on: August 17, 2015

17.4K

Area of Science:

  • Proteomics
  • Biomarker Discovery
  • Computational Biology

Background:

  • Quantitative proteomics often suffers from global intensity bias.
  • Accurate normalization is crucial for reliable differential expression analysis and biomarker identification.

Purpose of the Study:

  • To develop and validate a new normalization method for quantitative proteomics using endogenous protein standards (EPNS).
  • To assess the effectiveness of EPNS normalization in reducing bias and improving biomarker discovery for colorectal cancer.

Main Methods:

  • Developed a normalization strategy using endogenous protein expression levels as standards (EPNS).
  • Validated the method on tandem mass tag (TMT)-labeled proteomic datasets.
  • Employed differential protein expression analysis and machine learning (random forest) for biomarker identification.

Main Results:

  • EPNS normalization significantly reduced global intensity bias in proteomic data.
  • The coefficient of variation (CV) of the median was reduced by 55% and 82% on average.
  • Identified five proteins (NUP205, GTPBP4, CNN2, GNL3, S100A11) correlating with colorectal cancer.
  • Random forest models achieved a maximum AUC of 0.9998 with EPNS-normalized data, outperforming raw data (AUC 0.9739).

Conclusions:

  • The EPNS normalization method effectively mitigates global intensity bias in quantitative proteomics.
  • EPNS normalization enhances the performance of machine learning models for disease biomarker discovery.
  • This method is a valuable tool for accurate quantitative proteomic analysis and biomarker identification.