amsrpm: Robust Point Matching for Retention Time Aligment of LC/MS Data with R

Marc Kirchner, Benjamin Saussen, Hanno Steen, Judith A. J. Steen and Fred A. Hamprecht

Journal of Statistical Software, 2007, vol. 018, issue i04

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.

Date: 2007-01-10
References: View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.jstatsoft.org/index.php/jss/article/view/v018i04/v18i04.pdf
https://www.jstatsoft.org/index.php/jss/article/do ... 04/amsrpm_1.2.tar.gz
https://www.jstatsoft.org/index.php/jss/article/do ... v018i04/v18i04.R.zip

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:jss:jstsof:v:018:i04

DOI: 10.18637/jss.v018.i04

Access Statistics for this article

Journal of Statistical Software is currently edited by Bettina Grün, Edzer Pebesma and Achim Zeileis

More articles in Journal of Statistical Software from Foundation for Open Access Statistics
Bibliographic data for series maintained by Christopher F. Baum ().