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Updated: Jun 29, 2026

Low Molecular Weight Protein Enrichment on Mesoporous Silica Thin Films for Biomarker Discovery
Published on: April 17, 2012
Adaptive bandwidth selection for biomarker discovery in mass spectrometry
Bernd Fischer1, Volker Roth, Joachim M Buhmann
1ETH Zürich, Institute of Computational Science, Universitätstrasse 6, 8092 Zürich, Switzerland. bernd.fischer@inf.ethz.ch
Objective:
Differential quantification of proteins by liquid chromatography/mass spectrometry requires the alignment of a retention time axis. The alignment automatically corrects for time changes in the liquid chromatography unit when repeating two experiments.
Methods:
In this paper we will show an extension of non-negative canonical correlation analysis. We introduce an adaptive scale space estimation that adapts the complexity of a monotone regression function to the density of measurements across the retention time. Furthermore, a global model selection of the scale is replaced by a local one, where we estimate the scale for each individual time axis, instead of a global parameter that holds for all time axes.
Results:
We show in experiments that we got a 13% gain. The performance gain is measured in the number of proteins that are detected to differ significantly in abundance for two different biological samples.
Conclusion:
We conclude that the adaptive scale estimation and the local model selection can outperform the global model selection which yields a more effective selection of differentially abundant proteins.
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