Help please: having trouble converting Waters MRM raw data to mzXML
Harry
I was trying to use the mzXML conversion tool in PPT to convert some
MRM raw data acquired on a Waters Xevo through direct infusion. The
program could not do it. Has anybody had similar problem?
Thank you for any ideas and suggestions.
Harry
Joseph Slagel
What error did you get? Did it look anything like:
[Tue Jan 31 12:33:25 2012] EXECUTING: c:\Inetpub\tpp-bin\ReAdW -v --
mzXML c:/Inetpub/wwwroot/ISB/data/12032011_60min_PaG_XC_HP101_01.raw
The system cannot find message text for message number 0x2331 in the
message file for Application.
If so, then please try using msconvert instead of ReAdW. We're no longer supporting or bundling this program with TPP.
-Joe
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Harry
Thank you for replying my question.
The error message I got looks like this:
...
Preprocessing function 97
!!Warning!!: ignoring function 97 with type MRM
Preprocessing function 98
!!Warning!!: ignoring function 98 with type MRM
Preprocessing function 99
!!Warning!!: ignoring function 99 with type MRM
no scans found, exiting with error
END OUTPUT
RETURN CODE:65280
###### End Command Execution ######
# All finished at Tue Jan 31 10:57:14 2012
# END COMMAND BLOCK
I also tried msconvert. The program did generate a mzXML file from
the raw data, but there is no actual data (MRM transitions and their
signal intensities) in the mzXML file. Would it be more useful to you
to see the problem if I send you the mzXML file?
Thank you for your time.
Harry
On Jan 31, 10:40 am, Joseph Slagel <Joseph.Sla...@systemsbiology.org>
wrote:
Joseph Slagel
I'm not sure I can be of any more help. I'd suggest you forward your question to the ProteoWizard's mailing list (proteowiza...@lists.sourceforge.net) and I'm sure you'll get a answer.
-Joe
Matthew Chambers
TPP work with mzML chromatograms yet?
-Matt
On 2/1/2012 3:35 PM, Joseph Slagel wrote:
> Harry,
>
> I'm not sure I can be of any more help. I'd suggest you forward your question to the ProteoWizard's
> mailing list (proteowiza...@lists.sourceforge.net
> <mailto:proteowiza...@lists.sourceforge.net><mailto:sup...@proteowizard.org>) and I'm sure
> you'll get a answer.
>
> -Joe
>
>
> On Tue, Jan 31, 2012 at 11:18 AM, Harry <mrl...@gmail.com <mailto:mrl...@gmail.com>> wrote:
>
> Hello Joe,
>
> Thank you for replying my question.
>
> The error message I got looks like this:
>
> ...
> Preprocessing function 97
> !!Warning!!: ignoring function 97 with type MRM
> Preprocessing function 98
> !!Warning!!: ignoring function 98 with type MRM
> Preprocessing function 99
> !!Warning!!: ignoring function 99 with type MRM
> no scans found, exiting with error
> END OUTPUT
> RETURN CODE:65280
> ###### End Command Execution ######
> # All finished at Tue Jan 31 10:57:14 2012
> # END COMMAND BLOCK
>
> I also tried msconvert. The program did generate a mzXML file from
> the raw data, but there is no actual data (MRM transitions and their
> signal intensities) in the mzXML file. Would it be more useful to you
> to see the problem if I send you the mzXML file?
>
> Thank you for your time.
>
> Harry
>
> On Jan 31, 10:40 am, Joseph Slagel <Joseph.Sla...@systemsbiology.org
> <mailto:Joseph.Sla...@systemsbiology.org>>
Joseph Slagel
That's not an msconvert warning. Msconvert would handle his MRM data fine as mzML, not mzXML. Does TPP work with mzML chromatograms yet?
-Matt
On 2/1/2012 3:35 PM, Joseph Slagel wrote:
Harry,
I'm not sure I can be of any more help. I'd suggest you forward your question to the ProteoWizard's
mailing list (proteowizard-support@lists.sourceforge.net<mailto:proteowizard-support@lists.sourceforge.net><mailto:sup...@proteowizard.org>) and I'm sure
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David Shteynberg
On Wed, Feb 1, 2012 at 1:42 PM, Joseph Slagel
<Joseph...@systemsbiology.org> wrote:
> Come to think of it I don't believe we do.
>
>
> On Wed, Feb 1, 2012 at 1:40 PM, Matthew Chambers <matt.ch...@gmail.com>
> wrote:
>>
>> That's not an msconvert warning. Msconvert would handle his MRM data fine
>> as mzML, not mzXML. Does TPP work with mzML chromatograms yet?
>>
>> -Matt
>>
>>
>>
>> On 2/1/2012 3:35 PM, Joseph Slagel wrote:
>>>
>>> Harry,
>>>
>>> I'm not sure I can be of any more help. I'd suggest you forward your
>>> question to the ProteoWizard's
>>> mailing list (proteowiza...@lists.sourceforge.net
>>>
>>> <mailto:proteowiza...@lists.sourceforge.net><mailto:sup...@proteowizard.org>)
>> To post to this group, send email to spctools...@googlegroups.com.
>> To unsubscribe from this group, send email to
>> spctools-discu...@googlegroups.com.
>> For more options, visit this group at
>> http://groups.google.com/group/spctools-discuss?hl=en.
>>
>
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Harry
Harry
On Feb 1, 1:35 pm, Joseph Slagel <Joseph.Sla...@systemsbiology.org>
wrote:
> Harry,
>
> question to the ProteoWizard's mailing list (
Harry
Thanks for the comments.
I tried converting the raw data to mzML instead of mzXML as well. It
didn't work. All I got in the mzML file is the column heads, but no
content.
Harry
On Feb 1, 1:40 pm, Matthew Chambers <matt.chamber...@gmail.com> wrote:
> That's not an msconvert warning. Msconvert would handle his MRM data fine as mzML, not mzXML. Does
> TPP work with mzML chromatograms yet?
>
> -Matt
>
> On 2/1/2012 3:35 PM, Joseph Slagel wrote:
>
>
>
>
>
>
>
> > Harry,
>
> > I'm not sure I can be of any more help. I'd suggest you forward your question to the ProteoWizard's
> > <mailto:proteowizard-supp...@lists.sourceforge.net><mailto:supp...@proteowizard.org>) and I'm sure
Matthew Chambers
-Matt
Harry
I'm using Excel to open the mzML/mzXML files. What I am trying to do
with the mzML/mzXML files is to extract just the MRM transitions and
their corresponding signal intensities and use my own MATLAB program
to do data analysis. I had been able to use the TPP to convert the
Thermo MRM raw data to mzXML files. But so far it has not been
working for the Waters MRM raw data.
Thanks,
Harry
On Feb 2, 11:05 am, Matthew Chambers <matt.chamber...@gmail.com>
wrote:
Matthew Chambers
tried it with a 60mb mzML and it froze indefinitely (waited 10 minutes). I don't understand how you
did it with mzXML either...did you decode the base64 in MATLAB?
I'll privately send you a modified mscat that will accept an optional --chromatograms argument and
will output all the chromatograms in an mzML file in fixed-column ASCII form. The output looks like:
SRM SIC Q1=130.1 Q3=71.1 sample=1 period=1 experiment=1 transition=0
0.0298 0.0606 0.0912 0.1218 0.1525 0.1832 0.2137 0.2444 ...
0.0000 0.0000 200.0000 0.0000 0.0000 0.0000 0.0000 0.0000 ...
I will commit this updated mscat to pwiz soon.
Hope this helps,
-Matt