Hallo,
not sure if it is of help for your problem but:
the Software RecalOfline from Thermo (should be part of FT-programs)
allows to split raw files according to the scan filter.
It is even mention that one should be able to run that program over
command line what never worked in my hands...(Thermo never takes such
bug reports serious anyway - and does something about it).
If your data-set is not to huge you might split up the *.raw and
convert them separately.
best
Dominik
On 15.11.2009, at 20:18, Andris wrote:
>
> Hi,
>
> This week I converted a number of Orbitrap Exactive files
> using the installed Xcalibur (Thermo Exactive 1.1) and the current
> ReadW (4.3.1).
>
> The resulting *.mzXML files had the msLevel="0", polarity="any". Also
> raw files contain scans from four different functions ESI+ full lock,
> ESI+ full MZ, ESI- full lock and ESI- full MZ. All scans from these
> functions are merged in one mzXML file. Is it possible to split them
> in separate files or at least set correct values for "msLevel" and
> "polarity"?
> I can use a "filterLine" values for these task, but it requires extra
> coding and hassle.
>
> filterLine="FTMS {1;1} + p ESI Full lock ms [60.00-1200.00]"
>
> <?xml version="1.0" encoding="ISO-8859-1"?>
> <mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/
> mzXML_3.1"
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
> xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/
> mzXML_3.1 http://sashimi.sourceforge.net/schema_revision/mzXML_3.1/
> mzXML_idx_3.1.xsd"
>>
> <msRun scanCount="5214" startTime="PT0.10327S" endTime="PT2761.43S" >
> <parentFile fileName="649_MeOH_A_1sliced.raw" fileType="RAWData"
> fileSha1="ae4d528dc6142883f92eb0bbd5f5506cce01b904" />
> <msInstrument>
> <msManufacturer category="msManufacturer" value="Thermo Finnigan" /
>>
> <msModel category="msModel" value="unknown" />
> <msIonisation category="msIonisation" value="NSI" />
> <msMassAnalyzer category="msMassAnalyzer" value="FTMS" />
> <msDetector category="msDetector" value="unknown" />
> <software type="acquisition" name="Xcalibur"
> version="1.1-133400/1.1.0.1335" />
> </msInstrument>
> <dataProcessing>
> <software type="conversion" name="ReAdW" version="4.3.1(build Sep
> 9 2009 12:30:29)" />
> </dataProcessing>
> <scan num="1"
> msLevel="0"
> peaksCount="0"
> polarity="any"
> scanType="unknown"
> filterLine="FTMS {1;1} + p ESI Full lock ms [60.00-1200.00]"
> retentionTime="PT0.10327S"
> lowMz="0"
> highMz="0"
> basePeakMz="205.159"
> basePeakIntensity="94589.4"
> totIonCurrent="513978" >
> <peaks precision="32"
> byteOrder="network"
> contentType="m/z-int"
> compressionType="none"
> compressedLen="0" >AAAAAAAAAAA=</peaks>
> </scan>
>
> If somebody wants to investigate that,
> I can upload a raw file.
>
> Best regards,
>
> Andris
>
> >
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