I'm not new to MS and proteomics...but I'm relatively computer dumb
and command prompts scare me, which is why the IPP is interesting to
me over the TPP (which I have had so many permission errors during
setup that I'm overly frustrated). So thankfully, the IPP install went
100x faster than the TPP setup. YEAH!

So...I want to use the IPP to do the Sequest search as well. I have
Bioworks on the same computer as the IPP. I have no problem converting
my .RAW data to mzXML. Though, while it should be obvious, I have been
unable to find a tutorial or instructions on where to put the FASTA
databases (i.e which directory/folder) do they go into. And also, do I
start with the params file in the tutorial data and just edit this?
I've tried searching this google group, as well as the TPP wiki but
either I"m not searching correctly, or I'm the only one dumb enough to
not figure this out.

What is the easiest way to do all this?  And please, feel free to
speak in very simple terms, easier the better for me.

Thanks!!
Rebekah

Glad to hear the setup went well.  The good news is that all the work we put
into IPP has been put back into TPP, so in upcoming releases TPP should
install just as readily (they're going to use our improvements to dump
Cygwin, for one thing).  In future, you'll be better off working with TPP
since it's more actively supported by the community and by Insilicos.  But
for now, let's proceed with IPP.

I'm not a Sequest user, but as I understand the use of TPP/IPP with Sequest
it's largely a question of configuring Bioworks to work within the directory
structure desired by TPP.  This means your files (fasta, raw, mzXML, search
result, sequest.params etc) should all be located somewhere below
c:\Inetpub\wwwroot\ISB\data.  The sequest.params files should be faked up to
match the sequest search parameters you used, unless Bioworks actually
produces one on its own (I have the impression it's an antique file format,
but I'm uncertain).

Admittedly I'm faking it here, but hopefully we can fumble through together.
You could probably post to spctools-discuss and get a more coherent answer
which would still be applicable to IPP (but do couch it in TPP terms to
avoid a grouchy response).

Brian Pratt