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Bioinformatics Advance Access originally published online on May 6, 2005
Bioinformatics 2005 21(14):3066-3073; doi:10.1093/bioinformatics/bti482
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Published by Oxford University Press 2005

Algorithms for alignment of mass spectrometry proteomic data

Neal Jeffries

National Institute of Neurological Disorders and Stroke, National Institutes of Health Bethesda, MD 20892, USA

Motivation: The analysis of biological samples with high-throughput mass spectrometers has increased greatly in recent years. As larger datasets are processed, it is important that the spectra are aligned to ensure that the same protein intensities are correctly identified in each sample. Without such an alignment procedure it is possible to make errors in identifying the signals from peptides with similar molecular weight. Two algorithms are provided that can improve the alignment among samples. One algorithm is designed to work with SELDI data produced from a Ciphergen instrument, and the other can be used with data in a more general format.

Results: The two algorithms were applied to samples drawn from a common pool of reference serum. The results indicate substantial improvement in consistently identifying peptide signals in different samples.

Availability: The two algorithms are programmed using the R language and are available from http://krisa.ninds.nih.gov/alignment/

Contact: neal.jeffries{at}nih.gov

Received on March 13, 2005; revised on April 15, 2005; accepted on May 1, 2005

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[Abstract] [Full Text] [PDF]


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