Variance component analysis to assess protein quantification in biomarker validation: application to selected reaction monitoring-mass spectrometry

BMC Bioinformatics
Amna KlichPascal Roy

Abstract

In the field of biomarker validation with mass spectrometry, controlling the technical variability is a critical issue. In selected reaction monitoring (SRM) measurements, this issue provides the opportunity of using variance component analysis to distinguish various sources of variability. However, in case of unbalanced data (unequal number of observations in all factor combinations), the classical methods cannot correctly estimate the various sources of variability, particularly in presence of interaction. The present paper proposes an extension of the variance component analysis to estimate the various components of the variance, including an interaction component in case of unbalanced data. We applied an experimental design that uses a serial dilution to generate known relative protein concentrations and estimated these concentrations by two processing algorithms, a classical and a more recent one. The extended method allowed estimating the variances explained by the dilution and the technical process by each algorithm in an experiment with 9 proteins: L-FABP, 14.3.3 sigma, Calgi, Def.A6, Villin, Calmo, I-FABP, Peroxi-5, and S100A14. Whereas, the recent algorithm gave a higher dilution variance and a lower technical varianc...Continue Reading

References

Oct 16, 2008·Molecular Systems Biology·Vinzenz LangeRuedi Aebersold
Mar 28, 2009·Biostatistics·J E Eckel-PassowH R Bergen
Apr 4, 2009·Journal of Proteomics·Virginie BrunAlain Dupuis
Dec 17, 2009·The Journal of Animal Ecology·Andy HectorBernhard Schmid
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May 24, 2012·Expert Review of Molecular Diagnostics·Jérôme LemoineGeneviève Choquet-Kastylevsky

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BETA
ELISA

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SRMstats

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