Introduction

MOTIVATION: Proteomics has particularly evolved to become of high interest for the field of biomarker discovery and drug development. Especially the combination of liquid chromatography and mass spectrometry (LC/MS) has proven to be a powerful technique for analyzing protein mixtures. Clinically orientated proteomic studies will have to compare hundreds of LC/MS runs at a time. In order to compare different runs, sophisticated preprocessing steps have to be performed. An important step is the retention time (rt) alignment of LC/MS runs. Especially non-linear shifts in the rt between pairs of LC/MS runs make this a crucial and non-trivial problem. RESULTS: For the purpose of demonstrating the particular importance of correcting non-linear rt shifts, we evaluate and compare different alignment algorithms. We present and analyze two versions of a new algorithm that is based on regression techniques, once assuming and estimating only linear shifts and once also allowing for the estimation of non-linear shifts. As an example for another type of alignment method we use an established alignment algorithm based on shifting vectors that we adapted to allow for correcting non-linear shifts also. In a simulation study, we show that rt alignment procedures that can estimate non-linear shifts yield clearly better alignments. This is even true under mild non-linear deviations. AVAILABILITY: R code for the regression-based alignment methods and simulated datasets are available at http://www.statistik.tu-dortmund.de/genetik-publikationen-alignment.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Publications

  1. Retention time alignment algorithms for LC/MS data must consider non-linear shifts.
    Cite this
    Podwojski K, Fritsch A, Chamrad DC, Paul W, Sitek B, Stühler K, Mutzel P, Stephan C, Meyer HE, Urfer W, Ickstadt K, Rahnenführer J, 2009-03-01 - Bioinformatics (Oxford, England)

Credits

  1. Katharina Podwojski
    Developer

  2. Arno Fritsch
    Developer

  3. Daniel C Chamrad
    Developer

  4. Wolfgang Paul
    Developer

  5. Barbara Sitek
    Developer

  6. Kai Stühler
    Developer

  7. Petra Mutzel
    Developer

  8. Christian Stephan
    Developer

  9. Helmut E Meyer
    Developer

  10. Wolfgang Urfer
    Developer

  11. Katja Ickstadt
    Developer

  12. Jörg Rahnenführer
    Investigator

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Summary
AccessionBT001486
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByJörg Rahnenführer