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Related Experiment Video

Updated: May 21, 2026

Quantitative Analysis of Chromatin Proteomes in Disease
08:11

Quantitative Analysis of Chromatin Proteomes in Disease

Published on: December 28, 2012

Label-free protein quantitation using weighted spectral counting.

Christine Vogel1, Edward M Marcotte

  • 1Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA.

Methods in Molecular Biology (Clifton, N.J.)
|June 6, 2012
PubMed
Summary
This summary is machine-generated.

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This study introduces APEX, a novel method for calculating absolute protein expression levels from mass spectrometry data. APEX corrects for peptide detectability, enabling accurate protein quantification in complex biological samples.

Area of Science:

  • Proteomics
  • Biochemistry
  • Computational Biology

Background:

  • Mass spectrometry (MS)-based shotgun proteomics is crucial for identifying proteins in complex biological samples.
  • Estimating protein abundance from MS/MS spectral counts requires correction for peptide MS-detectability.
  • Existing methods may not fully account for variations in peptide detection across different proteins.

Purpose of the Study:

  • To introduce APEX (Absolute Protein EXpression), a new method for calculating absolute protein expression levels.
  • To address the challenge of differential MS-detectability of peptides in quantitative proteomics.
  • To provide a robust approach for accurate protein abundance estimation in complex proteomic datasets.

Main Methods:

  • APEX utilizes a machine learning model trained on peptide sequences and properties to estimate MS-detectability (O(i)).

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Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level
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Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level

Published on: April 19, 2019

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Related Experiment Videos

Last Updated: May 21, 2026

Quantitative Analysis of Chromatin Proteomes in Disease
08:11

Quantitative Analysis of Chromatin Proteomes in Disease

Published on: December 28, 2012

Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level
08:29

Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level

Published on: April 19, 2019

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

  • Absolute protein abundances are calculated using spectral counts, protein identification probabilities, and learned O(i) values.
  • Statistical analysis is incorporated for significance testing of differential protein expression between samples.

    • Main Results:

    • The APEX method successfully calculates absolute protein expression levels.
    • It effectively corrects for variations in peptide MS-detectability, improving quantification accuracy.
    • APEX-derived protein abundances span over four orders of magnitude and are applicable to diverse organisms.

    Conclusions:

    • APEX provides a reliable method for determining absolute protein expression from MS/MS spectral counts.
    • The approach enhances the accuracy of quantitative proteomics by accounting for peptide detectability.
    • APEX is a versatile tool applicable to complex biological mixtures and large-scale proteomic studies.