Journal Article

ChromA: signal-based retention time alignment for chromatography–mass spectrometry data

Nils Hoffmann and Jens Stoye

in Bioinformatics

Volume 25, issue 16, pages 2080-2081
Published in print August 2009 | ISSN: 1367-4803
Published online June 2009 | e-ISSN: 1460-2059 | DOI: https://dx.doi.org/10.1093/bioinformatics/btp343

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Summary: We describe ChromA, a web-based alignment tool for chromatography–mass spectrometry data from the metabolomics and proteomics domains. Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions. Additionally, user-defined anchors can be used to constrain and speedup the alignment. A neighborhood around each anchor can be added to increase the flexibility of the constrained alignment. ChromA offers different visualizations of the alignment for easier qualitative interpretation and comparison of the data. For the multiple alignment of more than two data files, the center-star approximation is applied to select a reference among input files to align to.

Availability: ChromA is available at http://bibiserv.techfak.uni-bielefeld.de/chroma. Executables and source code under the L-GPL v3 license are provided for download at the same location.

Contact: stoye@techfak.uni-bielefeld.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1380 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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