Quantitation

[kash]

Hi
i want to know whether all TPP upgrades will be included in IPP and i
am interested in quantitation proteomics, ASAPRatio and XPRESS. How
much streamlined or userfriendly is your interphase?
thanks
kash

[Bryan Prazen]

Kash,

Thank you for your interest in IPP.   All upgrades to TPP will be included in the IPP.  In some cases features will appear in the TPP releases before IPP.  This is because Insilicos will not release new features until they are tested here and the code is considered stable.  To date IPP has focused on software engineering and not made substantial changes to the interface.

In the area of ASAPRatio and XPRESS, we have made important improvements to the way these tools work with Mascot data.  Previously users found direct analysis of data in the MS manufactures format using Mascot Distiller resulted in more peptide and protein identifications then analysis routes that include conversion to mzXML before Mascot analysis, but quantitation using ASAPRatio and XPRESS was not successful if the MS manufacturer's format was fed directly into Mascot.  IPP understands Masscot Distiller data and gives correct ASAPRatio and XPRESS results if Mascot Distiller reads the MS manufacturer's format.  Thus, IPP user obtain the best list of identified peptides and quantition.  Also, IPP allows users to submit Mascot experiments that include multiple mzXML files.

I hope this helps,
Bryan Prazen
www.insilicos.com

[kash]

Thank you very much for the immediate response.
I am running Sequest search for my data. I will try your trial version
and is it possible to get a quote for IPP? We are a academic
institution.
One question about the TPP new interphase Gale 2.9.4, Did you check the
ASAPRatio and XPRESS, in this release? are the codes stable?
thanks
Kash

[Brian Pratt]

Hi Kash,

Our process involves keeping a parallel copy of the TPP code on our own source control repository, and carefully merging changes
from the public TPP repository into our own, reviewing each one carefully as we go. Then we perform regression testing on the
rebuilt IPP to make sure that nothing has been broken. This kind of software testing is a service of the IPP that you don't get
with the TPP. So while we don't monitor the stability of TPP directly, when we do detect a change in IPP behavior it's usually due
to some change in the TPP code, so we are tracking TPP stability indirectly. For example our automated tests recently pointed out a
fairly large change in the way Mascot files are handled that breaks the TPP for many users. This code had already made its way
into the TPP Gale 2.9.4 release. The change is actually useful for some users, so I'm now working with the author of that change
and the guys at the ISB to get it fixed in the TPP code so that everyone is happy, but the point is that users of the IPP are spared
the churning due to code changes that may not be completely thought out or tested.

To your specific question about ASAPRatio and XPRESS - I'm currently in the midst of one of our periodic synchronizations of the IPP
code with the latest TPP code. I haven't yet found any problems in ASAPRatio or XPRESS, although there have been changes to that
code so I'm proceeding carefully, and would not be surprised to find differences between the results from TPP 2.9.4 and previous
versions. Note that I said "differences", not "problems" - keep in mind that regression testing is only about detecting changes in
program behavior, so once such changes are detected we have to decide whether or not they're good changes. For example, there are
recent changes in the ASAPRatio code that make it report M+H instead of M, so this is a change but probably a good change since
that's how XPRESS reports its results. The main point is, with IPP you have a team watching out for these things.

Hope this helps,

Brian Pratt
www.insilicos.com/IPP.html

[Hank]

Hello, Kash,

Thanks for the quote request. I am happy to provide you with a quote
outside of this group discussion. To get thing rolling, can you contact
me directly at henry....@insilicos.com or call 206 295 1639?

Thanks for your interest in IPP.

Best regards,
Henry Turner

[kash]

Hi Bryan
i downloaded IPP, but couldnt use it. I checked your instructions in
the tutorial but couldnt get a clue.
I have TPP already running in my system.
DO i have to change anything in the environment variable, path? Let me
know
Thanks
Kash

[Bryan Prazen]

Kash,
You should not have to change anything and IPP should run along side TPP without interfering.  That said, everyone's system is different and it is possible that there was a problem with the installation.  Did you get an Insilicos Proteomics Pipeline shortcut on your desktop?  Were you the Windows administrator when you did the installation?  You should be able to click on it to call up IPP.  If this is not working what do you get when you open a DOS shell (Click the Windows Start menu select Run and type 'cmd' in the Open box) and type 'which xinteract.exe'? Also what to you get when you open a browser and type 'http://localhost'?

thanks,

bryan

On 10/26/06, kash <vishw...@gmail.com> wrote: