Coherent pipeline for biomarker discovery using mass spectrometry and bioinformatics

Background: Robust biomarkers are needed to improve microbial identification and diagnostics. Proteomics methods based on mass spectrometry can be used for the discovery of novel biomarkers through their high sensitivity and specificity. However, there has been a lack of a coherent pipeline connecting biomarker discovery with established approaches for evaluation and validation. We propose such a pipeline that uses in silico methods for refined biomarker discovery and confirmation. Results: The pipeline has four main stages: Sample preparation, mass spectrometry analysis, database searching and biomarker validation. Using the pathogen Clostridium botulinum as a model, we show that the robustness of candidate biomarkers increases with each stage of the pipeline. This is enhanced by the concordance shown between various database search algorithms for peptide identification. Further validation was done by focusing on the peptides that are unique to C. botulinum strains and absent in phyl...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Ali Al-Shahib, Raju Misra, Nadia Ahmod, Min Fang, Haroun Shah, Saheer Gharbia
• Keywords: Biomarker Discovery, BMCBI 2010, Peptides, Robust Biomarkers