Re: [proteowizard-support] Question about ProteoWizard

[Matthew C. <mat...@va...>]

Hi Kentar,

There's two problems with that file from pwiz's perspective:
1) index name for chromatograms is "chroms" - pwiz requires
"chromatogram". However, the valid values for that attribute are not
specified in the mzML_idx xsd
(http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/schema/mzML1.1.0_idx.xsd).
That's not acceptable, we might have to release a revision to specify
the two valid values for those attributes (although I suspect that
spectrum and chromatogram or spectra and chromatograms will be the
accepted identifiers).

2) The indexListOffset is wrong. It's 15340 when it should be 14875. It
might have something to do with Unix/DOS newlines, but if the file was
using DOS newlines, the correct index would be 15127, so it's still way off.

After I made those two fixes to the file, it read fine. I suspect OpenMS
and Mass++ ignore the index and so are immune to these issues, but since
pwiz takes advantage of it to speed up random access on large mzML
files, we are vulnerable. However, we should be able to deal with this
case of a "corrupt" index. So thank you for pointing out this issue, it
has brought to light several sub-issues! :)

Thanks,
-Matt


k2-...@hh... wrote:
> Hi Matt,
>
> I'm sending the data file.
> OpenMS and Mass++ can read this file.
>
> Thanks,
> Kentar
>
> ---
> Kentaro Matsuura
> Mailto: k2-...@hh...
> Voice: +81-298-47-5615  Fax: +81-298-47-7614
> Bioinformatics, Biomarkers and Personalized Medicine
> Eisai Product Creation Systems
> Eisai Co., Ltd.
>
> -----作成者: Matt Chambers <mat...@va...> -----
>
>
> 宛先: k2-...@hh...
> 送信者: Matt Chambers <mat...@va...>
> 日付: 2009/12/10 11:38
> cc: su...@pr..., s11...@hh...,
> k3-...@hh...
> 件名: Re: [proteowizard-support] Question about ProteoWizard
>
> I'll need to see the data file. Or really, the beginning and end of it.
> You can cut out all but the first and last spectrum, 7zip it, then
> attach it to email. And yes, you can get the source code from either SVN
> or from TeamCity (the pwiz-src tarball).
>
> Thanks,
> Matt
>
>
> k2-...@hh... wrote:
>   
>> Hi Matt,
>>
>> Thank you so much.
>> But, the tools still show the same error.
>>
>> And, I'd like to get source codes too.
>> Can I get them in the following URL?
>>
>> ~Kentar
>>     
> (See attached file: tiny.pwiz.1.1-2.mzML)