Hi Andris,
ReAdW gets the ms level and polarity from the filter line, but in this
case it doesn't know how to deal with the filter line so it seems to be
silently aborting the filter parser. The "extra coding and hassle"
should happen to the parser code instead of your own code (IMO). But in
this case, I'm not even sure what the elements of the scan filter mean.
What is {1;1}? What is "lock" vs. "MZ"? Is that like Waters's lock mass?
-Matt
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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