title: rapmad: Robust analysis of peptide microarray data.
abstract: BACKGROUND
  Peptide microarrays offer an enormous potential as a screening tool for peptidomics experiments and have recently seen an increased field of application ranging from immunological studies to systems biology. By allowing the parallel analysis of thousands of peptides in a single run they are suitable for high-throughput settings. Since data characteristics of peptide microarrays differ from DNA oligonucleotide microarrays, computational methods need to be tailored to these specifications to allow a robust and automated data analysis. While follow-up experiments can ensure the specificity of results, sensitivity cannot be recovered in later steps. Providing sensitivity is thus a primary goal of data analysis procedures. To this end we created rapmad (Robust Alignment of Peptide MicroArray Data), a novel computational tool implemented in R.
  
  
  RESULTS
  We evaluated rapmad in antibody reactivity experiments for several thousand peptide spots and compared it to two existing algorithms for the analysis of peptide microarrays. rapmad displays competitive and superior behavior to existing software solutions. Particularly, it shows substantially improved sensitivity for low intensity settings without sacrificing specificity. It thereby contributes to increasing the effectiveness of high throughput screening experiments.
  
  
  CONCLUSIONS
  rapmad allows the robust and sensitive, automated analysis of high-throughput peptide array data. The rapmad R-package as well as the data sets are available from http://www.tron-mz.de/compmed.
authors.affiliation: The Institute for Translational Oncology and Immunology (TrOn), 55131 Mainz, Germany.
authors.forename: Bernhard Y
authors.initials: BY
authors.lastname: Renard
authors.forename: Martin
authors.initials: M
authors.lastname: Löwer
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Kühne
authors.forename: Ulf
authors.initials: U
authors.lastname: Reimer
authors.forename: Andrée
authors.initials: A
authors.lastname: Rothermel
authors.forename: Ozlem
authors.initials: O
authors.lastname: Türeci
authors.forename: John C
authors.initials: JC
authors.lastname: Castle
authors.forename: Ugur
authors.initials: U
authors.lastname: Sahin
mesh_terms: D000465:Algorithms; D014408:Biomarkers, Tumor; D006801:Humans; D009369:Neoplasms / Q000378:metabolism*; D040081:Protein Array Analysis / Q000379:methods*; D012680:Sensitivity and Specificity; D012984:Software
chemical_list: D014408:Biomarkers, Tumor