I havent seen any replies to this so I am taking a shot (even though I am not even remotely the best qualified for the job).
Had started w/ long reply but thought the best tool for cmd automation for me was to run Petunia then capture cmd line and use that going forward. Cannot comment on 1) 4) (not good) and 5) but for 2) and 3) my biggest confusion is always keeping things straight on if one wishes to apply cmds on the protein or peptide level. So for me 2 (the cmds listed) would be done w/ ProteinProphet (as opposed to xinteract). These same conds.can be applied at the peptide level w/ diff. cmds using xinteract. This is how I view the pipeline (I am sure many are more sophistacated and knowledgeable in their approach) based on the Petunia display and the cmd line it generates. >From my understanding iProphet (which I really like) has additional stat. tools and can be used to feed ProteinProphet. PepProphet can feed both. All of these tools can be used to combine pep.xml files. So for me PepPro feeds IPro which then feeds ProPro Hope it helps and please anyone correct me where I am wrong. DD On Mar 4, 12:22 am, Simon Michnowicz <[email protected]> wrote: > Dear Group, > I have several questions about running xinteract, and I'd be grateful > if you could assist me. > (1) I ran xinteract on an angio file,( with limited spectra). > xinteract crashed at RefreshParser with a memory error. > failed to update simon-J1682.pepprophet.xml from temp file > simon-J1682.pepprophet.xml.tmp.94fG9b, error 12 "Cannot allocate > memory"). Is this a bug, and to whom do I report it? > (2) xinteract gives the option to call ProteinProphet. How do you > specify the protein prophet command line options form xtineract? (e.g. > ICAT GLYC XPRESS ASAP_PROPHET EXCLUDE_ZEROS PROTLEN PROTMW > DELUDE NOOCCAM NOGROUPS NORMPROTLEN INSTANCES GROUPWTS ) > (3) ProteinProphet can be called with several input files. If I used > Mascot to analyse many runs of a gel line, would I use ProteinProphet > to combine the results, or would I use iProphet, and then feed the > output of that to ProteinProphet? > (4)I naively put in some extra command line options for xinteract. I > added -TAA when I ran peptideProphet, and it exited immediately with > "with non-zero exit code: 11". Is this a problem? > (5)PeptideProphet command line options -i, -f are mutually exclusive. > is the absence of -i the same as the presence of -f? > > Thank you > Simon Michnowicz -- 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.
