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 Experiment Video

Updated: Jul 4, 2026

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions
09:00

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

Published on: April 18, 2025

Identifying differences in protein expression levels by spectral counting and feature selection.

P C Carvalho1, J Hewel, V C Barbosa

  • 1Programa de Engenharia de Sistemas e Computação, COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil. carvalhopc@cos.ufrj.br

Genetics and Molecular Research : GMR
|June 14, 2008
PubMed
Summary
This summary is machine-generated.

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

The Lorentz sphere visualised.

The Journal of chemical physics·2019
Same author

Lonomia obliqua bristle extract modulates Rac1 activation, membrane dynamics and cell adhesion properties.

Toxicon : official journal of the International Society on Toxinology·2019
Same author

GeLC-MS-based proteomics of Chromobacterium violaceum: comparison of proteome changes elicited by hydrogen peroxide.

Scientific reports·2016
Same author

Campomanesia adamantium extract induces DNA damage, apoptosis, and affects cyclophosphamide metabolism.

Genetics and molecular research : GMR·2016
Same author

Acrocomia aculeata prevents toxicogenetic damage caused by the antitumor agent cyclophosphamide.

Genetics and molecular research : GMR·2016
Same author

Individual differences in impulsive action and dopamine transporter function in rat orbitofrontal cortex.

Neuroscience·2015
Same journal

Diallel crosses for resistance to Macrophomina phaseolina and Thanatephorus cucumeris on cowpea.

Genetics and molecular research : GMR·2017
Same journal

Diversity among elephant grass genotypes using Bayesian multi-trait model.

Genetics and molecular research : GMR·2017
Same journal

Coupled transcript and metabolite identification: insights on induction and synthesis of resveratrol in peanut, wild relatives and synthetic allotetraploid.

Genetics and molecular research : GMR·2017
Same journal

Estimates of genetics and phenotypics parameters for the yield and quality of soybean seeds.

Genetics and molecular research : GMR·2017
Same journal

In silico modeling and characterization of phytoparasitic nematodes translationally-controlled tumor proteins.

Genetics and molecular research : GMR·2017
Same journal

Molecular identification of variety purity in a cotton hybrid with unknown parentage using DNA-SSR markers.

Genetics and molecular research : GMR·2017
See all related articles

Z-normalization and Support Vector Machine-Forward (SVM-F) correctly identified differentially expressed proteins in complex mixtures. This spectral counting data analysis method accurately quantifies protein concentrations and expression levels.

Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Bioinformatics

Background:

  • Spectral counting quantifies relative protein concentrations in complex mixtures using mass spectrometry.
  • Accurate identification of differentially expressed proteins is crucial for biological and clinical research.

Purpose of the Study:

  • To evaluate combinations of normalization and statistical methods for pinpointing differentially expressed proteins in spectral counting data.
  • To verify the effectiveness of these methods on controlled experimental data.

Main Methods:

  • Applied spectral counting on liquid chromatography-tandem mass spectrometry data from yeast lysates spiked with protein markers.
  • Evaluated normalization methods: total signal, Z-normalization, hybrid normalization, log preprocessing.

Related Experiment Videos

Last Updated: Jul 4, 2026

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions
09:00

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

Published on: April 18, 2025

  • Assessed feature selection methods: Golub index, Student t-test, SVM-F, SVM recursive feature elimination.

    • Main Results:

    • Z-normalization combined with the SVM-F method accurately identified the presence and quantity of spiked protein markers across different concentrations.
    • This combination proved effective in distinguishing differentially expressed proteins in complex samples.

    Conclusions:

    • The combination of Z-normalization and SVM-F is a robust strategy for analyzing spectral counting data.
    • This approach enhances the accuracy of identifying and quantifying differential protein expression in complex biological mixtures.