SOM-based Peptide Prototyping for Mass Spectrometry Peak Intensity Prediction

Scherbart A, Timm W, Böcker S, Nattkemper TW. SOM-based Peptide Prototyping for Mass Spectrometry Peak Intensity Prediction. In: Proceedings of the 6th Workshop on Self-Organizing Maps (WSOM 07). Bielefeld: Bielefeld University; 2007.In todays bioinformatics, Mass spectrometry (MS) is the key technique for the identification of proteins. A prediction of spectrum peak intensities from pre computed molecular features would pave the way to better understanding of spectrometry data and improved spectrum evaluation. We propose a neural network architecture of Local Linear Map (LLM)-type based on Self-Organizing Maps (SOMs) for peptide prototyping and learning locally tuned regression functions for peak intensity prediction in MALDI-TOF mass spectra. We obtain results comparable to those obtained by nu-Support Vector Regression and show how the SOM learning architecture provides a basis for peptide feature profiling and visualisation