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Improved parametric time warping for proteomics |
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| Authors: | Tom G Bloemberg Hans JP Wouters Maurice van Dael Lambert P van den Heuvel Paul HC Eilers Ron Wehrens |
| Affiliation: | a Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands b Nijmegen Proteomics Facility, Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic Diseases, Radboud University Nijmegen Medical Centre, The Netherlands c Nijmegen Centre for Mitochondrial Disorders, Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic diseases, Radboud University Nijmegen Medical Centre, The Netherlands d Department of Pediatrics, Radboud University Nijmegen Medical Centre, The Netherlands e Department of Biostatistics, Erasmus Medical Centre, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands |
| Abstract: | We present an improved version of parametric time warping, which enables the method to be used in LC-MS measurements in proteomics. The new features include a new similarity measure for comparing warped chromatograms, an insurance against peaks at the extremes of the chromatograms disappearing because of the warping, and the possibility to select and use multiple traces in searching the optimal alignment. Moreover, we present an alignment strategy combining global and individual alignments for aligning LC-MS data that exhibit different shifts within the same sample, at the same retention time. Using an LC-MS data set consisting of E. coli homogenates that were measured in several batches over a period of six months, we show the benefits of the improved algorithm and the merits of the new strategy. The algorithm is publicly available as the R package ptw. |
| Keywords: | Alignment Proteomics Parametric time warping R |
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