I do have Sequest/Bioworks on same computer as IPP. I am able to
convert my .RAW file to mzXML okay, but when I was trying to convert
them to pepXML through mascot search results. It take such a long time
to download them, and I can't convert to pep.xml, and protein prophet

I can't seem to win. I am thinking it's got to be something
fundamental I'm doing wrong, but am having problems finding a
where someone gives basic answer.

Thanks for any help.