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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
Submitted to Analytical Chemistry
Abstract
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
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