Published by the Foundation for Open Access Statistics Editors-in-chief: Bettina Grün, Torsten Hothorn, Edzer Pebesma, Achim Zeileis    ISSN 1548-7660; CODEN JSSOBK
Authors: Marc Kirchner, Benjamin Saussen, Hanno Steen, Judith A. J. Steen, Fred A. Hamprecht
Title: amsrpm: Robust Point Matching for Retention Time Aligment of LC/MS Data with R
Abstract: Proteomics is the study of the abundance, function and dynamics of all proteins present in a living organism, and mass spectrometry (MS) has become its most important tool due to its unmatched sensitivity, resolution and potential for high-throughput experimentation. A frequently used variant of mass spectrometry is coupled with liquid chromatography (LC) and is denoted as "LC/MS". It produces two-dimensional raw data, where significant distortions along one of the dimensions can occur between different runs on the same instrument, and between instruments. A compensation of these distortions is required to allow for comparisons between and inference based on different experiments. This article introduces the amsrpm software package. It implements a variant of the Robust Point Matching (RPM) algorithm that is tailored for the alignment of LC and LC/MS experiments. Problem-specific enhancements include a specialized dissimilarity measure, and means to enforce smoothness and monotonicity of the estimated transformation function. The algorithm does not rely on pre-specified landmarks, it is insensitive towards outliers and capable of modeling nonlinear distortions. Its usefulness is demonstrated using both simulated and experimental data. The software is available as an open source package for the statistical programming language R.

Page views:: 7196. Submitted: 2006-09-30. Published: 2007-01-10.
Paper: amsrpm: Robust Point Matching for Retention Time Aligment of LC/MS Data with R     Download PDF (Downloads: 7119)
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amsrpm_1.2.tar.gz: R source package Download (Downloads: 2665; 17KB)
v18i04.R.zip: v18i04.R: R example code from the paper Download (Downloads: 2121; 370B)

DOI: 10.18637/jss.v018.i04

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Paper: Creative Commons Attribution 3.0 Unported License
Code: GNU General Public License (at least one of version 2 or version 3) or a GPL-compatible license.