Some of the ASAP ratio values have large standard deviations. This tends to happen when the smoothed extracted ion chromatogram and the raw extracted ion chromatogram have large differences. Is there any way to filter the peptides with large standard deviations in ASAPratio prior to running ProteinProphet? The peptides with large standard deviations are throwing off my protein quant for peptides that are otherwise accurately detected and quantified.
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