Mixed-model of ANOVA for measurement reproducibility in proteomics

This work is a statistical analysis of reproducibility of a MALDI-TOF mass spectrometry experiment. Its aim is to evaluate measurement variability and compare peak intensities from two types of MALDI-TOF platforms. We compared and commented on the abilities of Principal Component Analysis and mixed-...

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Bibliographic Details
Published inJournal of proteomics Vol. 72; no. 6; pp. 974 - 981
Main Authors Mercier, Catherine, Truntzer, Caroline, Pecqueur, Delphine, Gimeno, Jean-Pascal, Belz, Guillaume, Roy, Pascal
Format Journal Article
LanguageEnglish
Published Netherlands Elsevier B.V 20.08.2009
Elsevier
Subjects
Adsorption
Analysis of Variance
ANOVA
Blood Proteins - chemistry
Computers
Experimental reproducibility
Hodgkin Disease - metabolism
Humans
Life Sciences
Mass Spectrometry - methods
Mixed models
Other
PCA
Peptides - chemistry
Principal Component Analysis
Proteome
Proteomics
Proteomics - methods
Quality Control
Reproducibility of Results
Software
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods
Variability
Experimental reproducibility
ANOVA
Variability
Mixed models
Proteomics
PCA
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Summary:This work is a statistical analysis of reproducibility of a MALDI-TOF mass spectrometry experiment. Its aim is to evaluate measurement variability and compare peak intensities from two types of MALDI-TOF platforms. We compared and commented on the abilities of Principal Component Analysis and mixed-model analysis of variance to evaluate the biological variability and the technical variability of peak intensities in different patients. The properties and hypotheses of both methods are summarized and applied to spectra from plasma of patients with Hodgkin lymphoma. Principal Component Analysis checks rapidly the balance between the two variabilities; however, a mixed-model analysis of variance is necessary to quantify the biological and technical components of the experimental variance as well as their interactions and to split the total variance into between-subjects and within-subject components. The latter method helped to assess the reproducibility of measurements from two MALDI-TOF platforms and to decompose the technical variability according to the experimental design.
ISSN:1874-3919
1876-7737
DOI:10.1016/j.jprot.2009.05.005