T. Rögnvaldsson, J. Häkkinen, C. Lindberg, G. Marko-Varga, F. Potthast, and J. Samuelsson
Improving Automatic Peptide Mass Fingerprint Protein Identification by Combining Multiple Peak Sets
to appear in J. Chromatography B

Several automatic peak detection strategies are presented and compared against manual peak picking, on a set of mass spectra obtained after tryptic in gel digestion of 2D-gel samples from human fetal fibroblasts. The spectra represent samples with both high and low protein abundance, and it is shown that peak sets selected by human operators have a considerable variability and that it is impossible to speak of a single true peak set. A completely automated peak detection strategy is developed that avoids time-consuming parameter tuning, and which yields protein identification efficiency that exceeds the human operator. The described method therefore allows automated user-independent protein identification using peptide mass fingerprints.

LU TP 03-04