I suspect it's a SIM/SRM data file so by default the SIM/SRM data is represented as chromatograms
instead of spectra. The --simAsSpectra/--srmAsSpectra flags should work to address that.
-Matt
On 7/26/2013 11:00 AM, Jimmy Eng wrote:
I would suggest that you follow-up with a post at the Skyline site requesting
the mzWiff binary.
Similarly, consider posting to the ProteoWizard support forum about your
problems using msconvert
on your wiff file; the developers there are pretty responsive to fixing any
problems that people
have with msconvert. Good luck.
On Fri, Jul 26, 2013 at 6:45 AM, <[email protected] <mailto:[email protected]>>
wrote:
msconvert (ProteoWizard 3.0.4743 32bit) should be able to do this, however,
I have difficulty in
using it to convert wiff files into mzXML. Every time, msconvert only
generates a small mzXML
(only 2kb) file which seems not contain any data (contents of a typical
generated mzXML file are
listed below). So I have to use mzWiff for this purpose. Could some one
please share a newer
mzWiff.exe with me or show me how to use msconvert correctly? I have
installed skyline on my
computer for msconvert. My OS is win7 64bit. Thanks.
<?xml version="1.0" encoding="ISO-8859-1"?>
<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2
http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_idx_3.2.xsd";>
<msRun scanCount="0" startTime="" endTime="">
<parentFile fileName="file://./Sample.wiff"
fileType="RAWData"
fileSha1="94a9c450ff213f4791de09da3ef867b9036e3b11"/>
<msInstrument msInstrumentID="1">
<msManufacturer category="msManufacturer" value="instrument model"/>
<msModel category="msModel" value="Applied Biosystems instrument
model"/>
<software type="acquisition" name="Analyst" version="unknown"/>
</msInstrument>
<dataProcessing>
<software type="conversion" name="ProteoWizard" version="3.0.4743"/>
<processingOperation name="Conversion to mzML"/>
</dataProcessing>
</msRun>
<sha1>ca60d7b35b33f31d4b0e2ca93192a3fdfad9aa0d</sha1>
</mzXML>
On Thursday, July 25, 2013 9:45:36 PM UTC-4, [email protected]
<mailto:[email protected]> wrote:
Could some one please share it with me ([email protected]
<mailto:[email protected]>) if
he/she has it? According the below link, such version was written on
2010, but I cannot find
a copy of it online. Many thanks.
Best,
Kang
https://skyline.gs.washington.__edu/labkey/announcements/home/__support/thread.view?entityId=__4ab351b9-8be0-102e-a614-__e08d31b97d89&_docid=thread%__3A4ab351b9-8be0-102e-a614-__e08d31b97d89
<https://skyline.gs.washington.edu/labkey/announcements/home/support/thread.view?entityId=4ab351b9-8be0-102e-a614-e08d31b97d89&_docid=thread%3A4ab351b9-8be0-102e-a614-e08d31b97d89>
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