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
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