Hi Luciana One tool that might fulfil criteria 1 would be Mayu that is also part of the TPP, see http://proteomics.ethz.ch/muellelu/web/LukasReiter/Mayu/ - it will calculate a new PSM score cutoff based on the input data (using the decoys) and compute a PSM score cutoff that is equivalent to a certain protein FDR.
Hannes On 1 April 2014 17:56, Luciana B <[email protected]> wrote: > Dear all, > > I have a dataset that I was trying to apply both peptide-level and > protein-level FDR. I have found some publications which set for example a > FDR below 1% for protein and peptide assignments, and I was wondering how it > was done. Can someone help me with this? > > 1. Is it possible to filter out peptides below the probability threshold (1% > FDR in PeptideProphet) before ProteinProphet analysis? In this case, only > the list of peptides matching this cutoff would be used to assemble the list > of proteins with ProteinProphet. > > 2. The other option would be filtering peptides after ProteinProphet, based > on the probabilities calculated in PeptideProphet. Is it possible? I have > noticed that ProteinProphet does not allow to filter out peptides based on > PeptideProphet calculated FDR. > > So, is it possible to apply both peptide-level FDR based on PeptideProphet > and protein-level FDR based on ProteinProphet, for the same dataset? > > Thank you!! > > Luciana > > > > > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
