Journal
PROTEOMICS
Volume 13, Issue 14, Pages 2083-2087Publisher
WILEY
DOI: 10.1002/pmic.201200518
Keywords
Autoantibodies; Bioinformatics; Biological markers; Parkinson's disease; Protein array analysis
Funding
- European Regional Development Fond (ERDF) of the European Union
- Ministerium fur Innovation, Wissenschaft und Forschung des Landes Nordrhein-Westfalen (ParkCHIP) [FZ 280381102]
- P.U.R.E. (Protein Unit for Research in Europe), a project of Nordrhein-Westfalen, a federal state of Germany
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Contemporary protein microarrays such as the ProtoArray (R) are used for autoimmune antibody screening studies to discover biomarker panels. For ProtoArray data analysis, the software Prospector and a default workflow are suggested by the manufacturer. While analyzing a large data set of a discovery study for diagnostic biomarkers of the Parkinson's disease (ParkCHIP), we have revealed the need for distinct improvements of the suggested workflow concerning raw data acquisition, normalization and preselection method availability, batch effects, feature selection, and feature validation. In this work, appropriate improvements of the default workflow are proposed. It is shown that completely automatic data acquisition as a batch, a reimplementation of Prospector's pre-selection method, multivariate or hybrid feature selection, and validation of the selected protein panel using an independent test set define in combination an improved workflow for large studies.
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