problem viewing spectra

[CH]

I'm having a problem viewing the spectra from any newly searched files
using TPP v3.4.0. I don't have a problem viewing spectra from
previously searched runs.

When I click on any link that directs me to a spectra, there's an
error message. The mzXML files are in the same folder as the .xml
files I'm viewing.

Examples:
Error - cannot read spectrum; tried direct .dta, from mzXML/mzData and
from .tgz (when clicking to see ions)

Error - cannot open file "xyz.mzXML".

Could not open input file xyz.mzXML Error In Reading xyz.mzXML (when
trying to open ASAPRatio: Peptide Ratio)

Any suggestions on what I can do?

Thanks for your time.

[Brian Pratt]

Can you provide more info - build number etc, Cygwin or Linux, etc?

[CH]

Cygwin I'm guessing since it's not Linux. Build number? TPP v3.4
SQUALL rev.0, Build 200711271744.

Anything else? Sorry, I'm not a computer person.

[Brian Pratt]

If you'll zip up that directory (with full path information) and upload to
ftp://insilicos.serveftp.net/pub/ I'd be happy to investigate.

Brian Pratt
www.insilicos.com

[CH]

Forgive my ignorance.

By directory you mean what exactly?

Appreciating your patience,
Christine

On Jan 29, 10:03 am, "Brian Pratt" <brian.pr...@insilicos.com> wrote:
> If you'll zip up that directory (with full path information) and upload toftp://insilicos.serveftp.net/pub/I'd be happy to investigate.

[Brian Pratt]

No problem: "directory" = "folder" in Windows-speak. By "full path
information" I mean the zip file should contain information about where the
folder is relative to everything else, so the files should have names like
"c:\inetpub\wwwroot\isb\data\foo\foo.mzXML" instead of just "foo.mzXML".

[CH]

I've uploaded the file CH_problem_viewing_spectra.zip.

Let me know if I've given you the files you're looking for.

On Jan 29, 10:03 am, "Brian Pratt" <brian.pr...@insilicos.com> wrote:
> If you'll zip up that directory (with full path information) and upload toftp://insilicos.serveftp.net/pub/I'd be happy to investigate.

[CH]

I see. I guess I didn't include the full path info. (C:\Inetpub
\wwwroot\ISB\data\tpp_newversiontest\3_4_0)

Did I send you the correct directory?

On Jan 29, 12:00 pm, "Brian Pratt" <brian.pr...@insilicos.com> wrote:
> No problem: "directory" = "folder" in Windows-speak. By "full path
> information" I mean the zip file should contain information about where the
> folder is relative to everything else, so the files should have names like
> "c:\inetpub\wwwroot\isb\data\foo\foo.mzXML" instead of just "foo.mzXML".
>
> -----Original Message-----
> From: spctools...@googlegroups.com
>
> [mailto:spctools...@googlegroups.com] On Behalf Of CH
> Sent: Tuesday, January 29, 2008 10:55 AM
> To: spctools-discuss
> Subject: Re: problem viewing spectra
>
> Forgive my ignorance.
>
> By directory you mean what exactly?
>
> Appreciating your patience,
> Christine
>
> On Jan 29, 10:03 am, "Brian Pratt" <brian.pr...@insilicos.com> wrote:
> > If you'll zip up that directory (with full path information) and upload

> toftp://insilicos.serveftp.net/pub/I'dbe happy to investigate.

[Brian Pratt]

Not a problem. I'd be curious to see the same data set as run through an
earlier, successful TPP version - can you send that? If that's not
possible, then just some other similarly sized data set from an earlier TPP
that worked for you will do.

Thanks,

Brian

[CH]

I've uploaded a file named CH_working_dataset.zip. It's the
same .mzXML file searched on TPP v3.2.1.

Full path c:\Inetpub\wwwroot\ISB\tpp_newversiontest\3_2_1

Christine

> > toftp://insilicos.serveftp.net/pub/I'dbehappy to investigate.

[Brian Pratt]

OK, that's helpful - the problem seems to be that the path information isn't
written to the pepXML file as it used to be:

<peptideprophet_summary version="PeptideProphet v3.0 April 1, 2004 (TPP v3.2
SQUALL rev.0, Build 200706191632)" author="AKeller@ISB" min_prob="0.05"
options=" MINPROB=0.05 EXTRAITRS=20 " est_tot_num_correct="233.5">
<inputfile
name="/cygdrive/c/Inetpub/wwwroot/ISB/data/tpp_newversiontest/3_2_1/cn109_si
lac_c_jl_rh_01"/>

<peptideprophet_summary version="PeptideProphet v3.0 April 1, 2004 (TPP v3.4
SQUALL rev.0, Build 200711271744)" author="AKeller@ISB" min_prob="0.05"
options=" MINPROB=0.05 EXTRAITRS=20 " est_tot_num_correct="240.6">
<inputfile name="cn109_silac_c_jl_rh_01"/>

Possibly this is due to a change somewhere in the TPP code, or possibly you
are doing something different without meaning to? Do you use the web
interface to drive the TPP?

[CH]

The problem I had earlier with view spectra temporarily solved itself,
but has now returned.

I have searched a single .mzXML file twice with the TPP GUI. The run
I searched last week had links to spectra, ions, and ASAPRAtio/XPRESS
ratios. The run I searched yesterday did have slightly different
search parameters but resulted in links that showed none of the
spectra I need to see. In the past however (see previous posts) the
different parameters for searching was not related to whether I could
see the spectra/ratios or not.

The errors I see
1. When clicking on ions: Error - Cannot read spectrum; tried

direct .dta, from mzXML/mzData and from .tgz

2. When clicking on ASAPRatio: Could not open input file
filename.mzXML. Error in reading filename.mzXML.
3. When clicking on XPRESS ratio: Error - cannot open file
"filename.mzXML."
4. When clicking on spectrum in Peptide/ProteinProphet: just lines of
text show up, no images.

I'm not sure if it makes a difference, but the mzXML file is in the
same folder that the .xml files are in for viewing the results.

Not sure why I'm the only one with this issue. Perhaps you can help
me figure out if I'm doing something wrong...

Thanks

> > > toftp://insilicos.serveftp.net/pub/I'dbehappyto investigate.