David, I was wondering if you could assist us with some information on the best way to merge files. I was of the understanding that InterProphet is for use when merging the outputs of different search algorithms, and that peptideProphet should be used to merge files searched by the same algorithm, e.g.
If you had M files, each searched using N algorithms, peptideProphet should be used to merge the M outputs of each search algorithm, and then N files merged together with InterProphet. I can't see IPROPHET in the option list of the Petunia interface for ProteinProphet (although it is listed in the command line). We have : TPP v4.4 JETSTREAM (unstable development prerelease) rev 0, Build 201007011135 (linux) Is there a newer version we should be using? Regards Simon Michnowicz Duty Programmer Australian Proteomics Computation Facility Ludwig Institute For Cancer Research Royal Melbourne Hospital, Victoria Tel: (+61 3) 9341 3155 Fax: (+61 3) 9341 3104 Topic: Limit of iProphet <http://groups.google.com/group/spctools-discuss/t/4fb27ad2e908192d> David Shteynberg <[email protected]> Sep 29 11:46AM -0700 ^ Hi Rachel, It is limited only by the amout of memory you have on your system. The memory req scales linearly with number of spectra being combined. Obviously the more spectra that are analysed together the better the statistics are going to be, but this too has a practical limit. Once you have the individual iProphet pepxmls you should not run iProphet on them again since you'll run into the same memory issue. Instead this is a perfect time to run ProteinProphet on the iProphet files and specify the IPROPHET option to make sure it uses iProphet probabilities. -David Rachel <[email protected]> Sep 29 06:04PM -0700 ^ Hi David, Thank you very much! Rachel :) On Sep 30, 2:46 am, David Shteynberg <[email protected]> wrote: -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en. This communication is intended only for the named recipient and may contain information that is confidential, legally privileged or subject to copyright; the Ludwig Institute for Cancer Research Ltd does not waive any rights if you have received this communication in error. The views expressed in this communication are those of the sender and do not necessarily reflect the views of the Ludwig Institute for Cancer Research Ltd. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
