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BMC Bioinformatics

, 6:203

First Online: 15 August 2005Received: 26 April 2005Accepted: 15 August 2005


BackgroundPeptide Mass Fingerprinting PMF is a widely used mass spectrometry MS method of analysis of proteins and peptides. It relies on the comparison between experimentally determined and theoretical mass spectra. The PMF process requires calibration, usually performed with external or internal calibrants of known molecular masses.

ResultsWe have introduced two novel MS calibration methods. The first method utilises the local similarity of peptide maps generated after separation of complex protein samples by two-dimensional gel electrophoresis. It computes a multiple peak-list alignment of the data set using a modified Minimum Spanning Tree MST algorithm. The second method exploits the idea that hundreds of MS samples are measured in parallel on one sample support. It improves the calibration coefficients by applying a two-dimensional Thin Plate Splines TPS smoothing algorithm. We studied the novel calibration methods utilising data generated by three different MALDI-TOF-MS instruments. We demonstrate that a PMF data set can be calibrated without resorting to external or relying on widely occurring internal calibrants. The methods developed here were implemented in R and are part of the BioConductor package mscalib available from

ConclusionThe MST calibration algorithm is well suited to calibrate MS spectra of protein samples resulting from two-dimensional gel electrophoretic separation. The TPS based calibration algorithm might be used to correct systematic mass measurement errors observed for large MS sample supports. As compared to other methods, our combined MS spectra calibration strategy increases the peptide-protein identification rate by an additional 5 – 15%.

AbbreviationsMMEmass measurement error

MSTminimum spanning tree.

MSMass Spectrometry.

TOFTime of Flight.

MALDIMatrix Assisted Laser Desorption Ionization.

modmodulo operator.

TPSThin plate spline.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-6-203 contains supplementary material, which is available to authorized users.

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Autor: Witold E Wolski - Maciej Lalowski - Peter Jungblut - Knut Reinert


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