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Journal Article

Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants

MPS-Authors

Wolski,  Witold E.
Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons81959

Jungblut,  Peter R.
Core Facilities / Proteinanalysis, Max Planck Institute for Infection Biology, Max Planck Society;

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Fulltext (public)

BMC_Bioinform_2005_6_203.pdf
(Publisher version), 965KB

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Citation

Wolski, W. E., Lalowski, M., Jungblut, P. R., & Reinert, K. (2005). Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants. BMC Bioinformatics, 6: 203.


Cite as: http://hdl.handle.net/11858/00-001M-0000-000E-C445-A
Abstract
Abstract Background Peptide 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. Results We 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 http://www.bioconductor.org. Conclusion The 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%.