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This article is part of the supplement: Neural Information Processing Systems (NIPS) workshop on New Problems and Methods in Computational Biology

Open Access Proceedings

Time-series alignment by non-negative multiple generalized canonical correlation analysis

Bernd Fischer12*, Volker Roth1 and Joachim M Buhmann12

Author Affiliations

1 Institute of Computational Science, ETH Zurich, Switzerland

2 Competence Center of Systems Physiology and Metabolic Diseases, ETH Zurich, Switzerland

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BMC Bioinformatics 2007, 8(Suppl 10):S4  doi:10.1186/1471-2105-8-S10-S4

Published: 21 December 2007



Quantitative analysis of differential protein expressions requires to align temporal elution measurements from liquid chromatography coupled to mass spectrometry (LC/MS). We propose multiple Canonical Correlation Analysis (mCCA) as a method to align the non-linearly distorted time scales of repeated LC/MS experiments in a robust way.


Multiple canonical correlation analysis is able to map several time series to a consensus time scale. The alignment function is learned in a supervised fashion. We compare our approach with previously published methods for aligning mass spectrometry data on a large proteomics dataset. The proposed method significantly increases the number of proteins that are identified as being differentially expressed in different biological samples.


Jointly aligning multiple liquid chromatography/mass spectrometry samples by mCCA substantially increases the detection rate of potential bio-markers which significantly improves the interpretability of LC/MS data.