Insilicos IPP Google Group

RE: [IPP list] How do I setup a Sequest search within the IPP?

brian.pr...@insilicos.com (Brian Pratt) — Thu, 17 Apr 2008 17:48:05 UT

Hi Ruby,
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

How do I setup a Sequest search within the IPP?

rgund...@jhmi.edu (Ruby) — Thu, 17 Apr 2008 16:30:22 UT

Hi -

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!

NSP bin

spctools2...@googlemail.com (research user) — Fri, 14 Mar 2008 18:05:38 UT

What is the role of NSP bin in the protein prophet results, how the
value is assigned to it and how that value should be interpreted for
concluding protien identifications.
I could understand the importance of NSP (number of sibling peptides) in
assigning a correct protein identification. My question is what is the need

Re: [IPP list] Re: IPP installation

bry...@insilicos.com (Bryan Prazen) — Mon, 03 Mar 2008 19:23:47 UT

Kanchan,
What you sent is the PepXML file info that I tried to describe earlier (I
think I told you to look for it under the tools tab). I do not believe that
IPP will work with pepXML data directly from the free Mascot server.
All of your problems appear to be related to the fact that IPP and TPP need

Re: [IPP list] Re: IPP installation

spctools2...@googlemail.com (research user) — Mon, 03 Mar 2008 14:41:02 UT

Dear Bryan,
Here I have one more query.
I have run a file in Mascot and got the output in pepxml format.
Now when I try to visualise this file with IPP it says
PepXML File: c:/Inetpub/wwwroot//ISB/kandat a/tppresults/jm.xml
Database: /home/matrix/site/sequence/NCB Inr/current/NCBInr_20080221.fa sta
Warning: Database is not in the expected location!

Re: [IPP list] Re: IPP installation

spctools2...@googlemail.com (research user) — Mon, 03 Mar 2008 14:06:32 UT

Dear Bryan,
Thanks for your mail, hopefuly you will be able to test the file today. Its
a file generated from TPP, i tried to open it up in IPP and it did not open.
I have few more questions now
I tried to run xtandem search with ipp
do i need to download x tandem to my computer, if so where it has to be

Re: [IPP list] Re: IPP installation

bry...@insilicos.com (Bryan Prazen) — Sun, 02 Mar 2008 01:54:53 UT

Kanchan,
I am unable to test this today, but I suspect that it might be that this
file was made with the cygwin build of TPP. Notice that all the paths start
with /cygdrive/c. If your using IPP, IPP is probably not able to find or
open the files in the cygwin directory structure. You could re-run the

Re: [IPP list] Re: IPP installation

spctools2...@googlemail.com (research user) — Sat, 01 Mar 2008 23:51:29 UT

Why do I get this message when I try to openup the result file from peptide
validation n pepxml viewer . i am able to open up other xml files in pepxml
viewer
the message says
*error with html display: XML parsing error: mismatched tag, at xml file
line 5, column 2*
I have attached the file here, if you are able to figure out the problem

Re: [IPP list] TPP and VISTA

bry...@insilicos.com (Bryan Prazen) — Fri, 29 Feb 2008 16:09:00 UT

Kanchan,
It sounds like you might have the TPP build available from the ISB's Seattle
Proteome Center because you are trying to connect to port 1441. I am not
sure how to get their build to run on Vista, but if you download IPP (
[link]) and follow the Vista
installation instructions (

TPP and VISTA

spctools2...@googlemail.com (spctools2008@googlemail.com) — Fri, 29 Feb 2008 15:00:17 UT

I have bought a new PC with windows vista, I am trying to install TPP
on it but so far I am unsuccessfull, please guide. I have TPP running
smoothly on my laptop with windows xp.
Do i need to download an apache server other than what comes with TPP.
I tried checking all the setting on both of my computers ( environment

Re: [IPP list] Re: IPP installation

spctools2...@googlemail.com (research user) — Mon, 25 Feb 2008 12:09:42 UT

Thanks, now I have installed the latest one and its working fine. I have
started the analysis, I will come back to you if I have some queries.
Kanchan
On Sat, Feb 23, 2008 at 4:50 AM, Brian Pratt <brian.pr...@insilicos.com>
wrote:

RE: [IPP list] Re: IPP installation

brian.pr...@insilicos.com (Brian Pratt) — Sat, 23 Feb 2008 04:50:12 UT

Oh my, thanks for letting me know about that. It would appear that a very
old version of that web page found its way back onto the website. Please
try the download again, you should get version 1.0.91 instead.

Thanks,

Brian Pratt

_____
On Behalf Of research user
Sent: Monday, February 18, 2008 7:33 AM

Re: [IPP list] Re: IPP installation

spctools2...@googlemail.com (research user) — Mon, 18 Feb 2008 15:32:45 UT

I have downloaded and installed the version ipp1-0-2.exe from
[link] web page. Please send me the link
if there is another latest version available.
thanks

RE: [IPP list] Re: IPP installation

brian.pr...@insilicos.com (Brian Pratt) — Mon, 18 Feb 2008 15:17:36 UT

I'd start by making sure you have the latest from the Insilicos website. It
sounds like you may be trying to run an older version? Also, if the web
page says 30 days free we need to fix that - it's just plain free now.
Thanks,
Brian Pratt
-----Original Message-----
On Behalf Of spctools2...@googlemail.com

Re: IPP installation

spctools2...@googlemail.com (spctools2008@googlemail.com) — Mon, 18 Feb 2008 13:08:47 UT

here is the path set under environment variables C:\Inetpub\ipp-bin;C:
\Perl\bin\;c:\Perl\bin;;C:\Pro gram Files\Java\jre1.6.0_03\bin;C:
\Program Files\QuickTime\QTSystem\;C:\c ygwin\usr\X11R6\bin;C:\cygwin
\bin
does this needs any changes, or does any other variable needs to be
changed or added.