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Evaluation of peak-picking algorithms for protein mass spectrometry

Bauer, C., Cramer, R. ORCID: and Schuchhardt, J. (2011) Evaluation of peak-picking algorithms for protein mass spectrometry. In: Hamacher, M., Eisenacher, M. and Stephan, C. (eds.) Data mining in proteomics: from standards to applications. Methods in molecular biology, 696. Humana Press, USA, pp. 341-352. ISBN 9781607619864

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To link to this item DOI: 10.1007/978-1-60761-987-1_22


Peak picking is an early key step in MS data analysis. We compare three commonly used approaches to peak picking and discuss their merits by means of statistical analysis. Methods investigated encompass signal-to-noise ratio, continuous wavelet transform, and a correlation-based approach using a Gaussian template. Functionality of the three methods is illustrated and discussed in a practical context using a mass spectral data set created with MALDI-TOF technology. Sensitivity and specificity are investigated using a manually defined reference set of peaks. As an additional criterion, the robustness of the three methods is assessed by a perturbation analysis and illustrated using ROC curves.

Item Type:Book or Report Section
Divisions:Life Sciences
Life Sciences > School of Chemistry, Food and Pharmacy > Department of Chemistry
ID Code:18352
Publisher:Humana Press
Publisher Statement:The original publication is available at


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