Hello, We have an orbitrap and the Proteome discoverer software that comes along with it. The results of these software seems ok but we need more manageable data to do some statistics on them. Thus I use TPP, but only with Mascot and Xtandem identifications (I haven't manage to use the proteome discoverer sequest identification..). I use the default parameters of peptide prophet and I tried various thresholds but the peptides identified are not the same as those found by proteome discoverer and there are less peptides kept with peptide prophet. We checked some of the peptides kept only by Proteome discover and they really are in the sample. Do you have any idea how to explain the difference between the results? Is the peptide prophet algorithm to much conservative for some type of data?
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