Re: [spctools-discuss] Creating / compiling a mzXML file from scratch - C# code available ?

[Brian Pratt]

The best thing would be to just use your new reader code to extend
msconvert so that it *does* read your file. Then you can output to
anything msconvert already handles.

- Brian Pratt

On Wed, Aug 8, 2012 at 8:40 AM, wlstraube <str...@imp.ac.at> wrote:
> Hello TPP-Team,
>
> I would like to compile a mzXML file from a Thermo raw-file, which has an
> internal structure that cannot be converted by msconvert.
> I am able to read out the raw-file and process it, but now want to save it
> as a mzXML.
>
> Therefore, without reinventing the wheel, I would like to know, where I can
> find the source code in C/ C++/ C# for a mzXML-compiler (preferably from the
> TPP project).
>
> Can anybody help me with that issue ?
>
> Best regards,
>
> Werner
>
>
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[wlstraube]

Dear Brian,

Thank you very much for the quick response.

If I get you right, I should take the msconvert source code and implement our code. This sounds logically, but for a first try I would try to keep it simple.

I would need only the part which writes down the required parameters. Would you be able (and kind) to provide me with that part?

Another option would be the old ReAdW converter source code. Any idea which file I would have to choose ?

( http://sashimi.svn.sourceforge.net/viewvc/sashimi/branches/readw_3_0/mzXML/converters/ReAdW/ )


With best regards,

Werner






.

[Brian Pratt]

For simplicity, you would probably want to go with the hacking up the
old readw code. But if you have any plans for sharing your work or
using it very far into the future then you're better off with
ProteoWizard and msconvert since that gets maintained and offers more
output formats.

Brian

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[kshitiz]

Hiya,

What about using ReAdW ? This is what we routinely use to convert RAW files to mzXML.

Cheers,

Kshitiz

[wlstraube]

Hello Kshitiz,

That I was asking in the post before. Due to a special method-setup in XCalibur - I cannot use ReADW directly for conversion.  We first have to read out the raw-files with our own software and then need to save the data again in a universal format, preferably mzXML format.

Therefore having the code for saving the parameters etc as as mzXML would be the easiest way for us (I guess).

Best,

Werner

[Matthew Chambers]

Hi Werner,

Assuming you eventually want to publish your method and have other people adopt it, the best thing
to do would be to make msconvert handle your RAW files. Having other users of your method be able to
use a widely adopted converter is better than creating a new ad-hoc solution.

I'm curious what you did in Xcalibur to make your files incompatible with msconvert. Can you share a
small example RAW file?

Thanks,
-Matt

[wlstraube]

Hello Matt,

There are actually more issues with msconvert.

(1) I have difficulties that msconvert correctly converts standard thermo-raw-file of QExactive runs. There seems to be that

   

    - scan data is corrupt (likely encoding problems)

    - Thermo filterline is missing (as specified by mzXML)

I have to admit that I used the graphical user interface (MSConvertGUI.exe), thus I am not sure, if this causes the problem.


(2) For the special raw-file format we obtain (and the reason I started the post), it is just about having several MS2 scans of the same precursor and then merging the MS2 spectra together.


Question: is the msconvert tool (what I think is a fantastic thing to have) currently maintained by someone and updated with latest formats ?


Best,

Werner

[Matthew Chambers]

1. We routinely use msconvert on QExactive data, so I'd need to see your data file to understand why
it's not working.

2. Yes, it is frequently updated and bugs that are reported are usually fixed within a week. I'm
curious why you didn't set the method to collect multiple microscans per MS2 (which get combined
automatically) instead of collecting independent MS2s? We've pondered having this kind of capability
in msconvert for older Waters data where the microscans were not automatically combined.

-Matt

[wlstraube]

Hello Matt,

We got it to work now, taking a detour but it works fine now. It was more a problem reading the mzXML files and then ignoring certain things.

However, I have one more question: Where is in the latest format of mzXML the isolation width of the precursor stored (set in the method of the instrument) ?

I was not able to find it. Is it stored at all ? (I found some old discussions, that it was not the case for previous versions).

Please understand, that I am currently not able to provide you with a data file, I would probably get in trouble....

Best regards,

Werner

[Matthew Chambers]

No I don't think isolation width is representable in mzXML except perhaps with the pseudo-CV
mechanism which pwiz/msconvert doesn't support for mzXML. You probably want to switch to mzML. It
has a considerably richer metadata model, including isolation width.

-Matt

[dominik]

Dear All,

I use MSconvert to convert *.raw from LTQ-Orbitrap acquisitions into
*.mzxml.
In comparison to the ReAdW converter MSconvert (using the GUI version)
does not include the Filterline.
Is it possible to maintain that in the conversion?

regards
Dominik

Example: ReAdW with filterline:

msLevel="1"
peaksCount="871"
polarity="+"
scanType="Full"
filterLine="FTMS + c NSI Full ms [360.00-900.00]"
retentionTime="PT0.1897S"
lowMz="360.264"
highMz="899.813"
basePeakMz="898.783"
basePeakIntensity="525343"
totIonCurrent="5.51739e+006" >

Example: MSconvert - no filterline
<scan num="1"
scanType="Full"
centroided="1"
msLevel="1"
peaksCount="1049"
polarity="+"
retentionTime="PT0.1884S"
lowMz="360.323303222656"
highMz="899.787109375"
basePeakMz="898.782836914063"
basePeakIntensity="4.3643228125e05"
totIonCurrent="5.356015e06"
msInstrumentID="1">

--
Dr. Dominik Schwudke
Group Leader

National Centre for Biological Sciences
Tata Institute of Fundamental Research
GKVK, Bellary Road,
Bangalore 560065, India

Phone +91-80 � 2366 6499
+91-80 - 6717 6499
dom...@ncbs.res.in

[dominik]

Dear All,

I look for an opportunity assign MS3 spectra as MS2.
Until now in the common converters I could not find such option.
I thought that in the past it was from time to time usually done to
merge MS2 and MS3. Even this option I could not find specifically in
MSconvert.
Could you please give me a hint if there is such option that I could
routinely convert *.raw files from LTQ-Orbitrap acquistion files to
mzXML and merge MS3 into MS2.

Thanks
Dominik

On 8/20/2012 10:42 PM, Matthew Chambers wrote: