#16 Waters DRE data loses functions when converting to mzML

[J Pearce]

Hi - we are haveing trouble converting Waters .raw data acquired with dynamic range extension into mzML (pwiz 3.0.11174-x86_64)

The raw files have four functions:
1) The stiched DRE function that combines 3 and 4)
2) The usual Waters lockmass
3) The high intesity scans
4) The low intesity scans

The mzML file produced only reproduces three of these functions (possibly becasue the stiched function shares the scan time with 3 or 4?):

Pwiz seems to be seeing fuction 1 when reading the file:

<run id="_x0034_fun_LTR" defaultInstrumentConfigurationRef="IC" startTimeStamp="2017-07-14T00:04:04Z" defaultSourceFileRef="_FUNC001.DAT">
<spectrumList count="6722" defaultDataProcessingRef="pwiz_Reader_Waters_conversion">

and:

<sourceFileList count="18">
<sourceFile id="_FUNC001.DAT" name="_FUNC001.DAT" location="file://C:\\Users\\aw4212\\Desktop\\RealTimeProcessingv3\\4fun_LTR.raw">
<cvParam cvRef="MS" accession="MS:1000769" name="Waters nativeID format" value=""/>
<cvParam cvRef="MS" accession="MS:1000526" name="Waters raw format" value=""/>
<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="71d7652cec80d1c645dfcbbbd59c6567ab3497b9"/>
</sourceFile>
<sourceFile id="_FUNC002.DAT" name="_FUNC002.DAT" location="file://C:\\Users\\aw4212\\Desktop\\RealTimeProcessingv3\\4fun_LTR.raw">
<cvParam cvRef="MS" accession="MS:1000769" name="Waters nativeID format" value=""/>
<cvParam cvRef="MS" accession="MS:1000526" name="Waters raw format" value=""/>
<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="69df410df4f87e41019b6d4752cabbf962723480"/>
</sourceFile>
<sourceFile id="_FUNC003.DAT" name="_FUNC003.DAT" location="file://C:\\Users\\aw4212\\Desktop\\RealTimeProcessingv3\\4fun_LTR.raw">
<cvParam cvRef="MS" accession="MS:1000769" name="Waters nativeID format" value=""/>
<cvParam cvRef="MS" accession="MS:1000526" name="Waters raw format" value=""/>
<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="cda529ad5bb38d78e3fe3ccec9140cf182f6961d"/>
</sourceFile>
<sourceFile id="_FUNC004.DAT" name="_FUNC004.DAT" location="file://C:\\Users\\aw4212\\Desktop\\RealTimeProcessingv3\\4fun_LTR.raw">
<cvParam cvRef="MS" accession="MS:1000769" name="Waters nativeID format" value=""/>
<cvParam cvRef="MS" accession="MS:1000526" name="Waters raw format" value=""/>
<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="937ecde200660ca2e5bf3c0a4beec0562d0fee97"/>
</sourceFile>

But fucntion 1 is not present in the data that is written out:

<index name="spectrum">
<offset idRef="function=2 process=0 scan=1">9530</offset>
<offset idRef="function=4 process=0 scan=1">47592</offset>
<offset idRef="function=3 process=0 scan=1">176175</offset>
<offset idRef="function=4 process=0 scan=2">187749</offset>
<offset idRef="function=3 process=0 scan=2">308856</offset>
<offset idRef="function=4 process=0 scan=3">319914</offset>
<offset idRef="function=3 process=0 scan=3">441062</offset>
<offset idRef="function=4 process=0 scan=4">451956</offset>
<offset idRef="function=3 process=0 scan=4">573023</offset>

Is there a way to either reproduce all functions in the mzML, or specify we only want to capture only the first function at conversion (simlar to filtering MS levels)?

Let me know if any example data files would help.

Jake

[J Pearce]

An update to say that the scanEvent filter does not help in this case - trying to only pass function 1 does not cause it to appear in the generated mzML.

An example raw file and derived mzML can be found here

[J Pearce]

Looks to be fixed in [r11498]