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Poll

What converter did you use?

Agilent MassHunter
[ 1 ] (7.1%)
Waters Databridge
[ 7 ] (50%)
Thermo - native converter
[ 0 ] (0%)
msConvert
[ 2 ] (14.3%)
CompassXport
[ 1 ] (7.1%)
Trapper
[ 0 ] (0%)
mzWiff
[ 0 ] (0%)
proteoWizard
[ 3 ] (21.4%)
Other - post to forum
[ 0 ] (0%)

Total Members Voted: 12

Voting closed: August 19, 2011, 12:07:55 PM

Topic: mz sorting violation (Read 9089 times) previous topic - next topic

mz sorting violation

I have noticed that a lot of people have been getting the mz sort violation error while processing their data. In an effort to know where this is coming from I've created a poll. If people who have had this problem could vote and let us know where and how they converted. Maybe it's a certain instrument/parameter/converter or totally random?

Paul
~~
H. Paul Benton
Scripps Research Institute
If you have an error with XCMS Online please send me the JOBID and submit an error via the XCMS Online contact page

Re: mz sorting violation

Reply #1 –
Hi,

We've now had the problem as well, on a Waters GC/MS.
The conversion included some Xcalibur peak picking, so that could be a culprit as well.
And the violating peak has an incredibly low intensity, so low it looks like a bug.

Yours,
Steffen

Code: [Select]
[305,] 322.72345 2.577887e-08
[306,] 323.53979 1.403037e-05
[307,] 324.79047 5.404045e+02
[308,] 178.08965 2.829593e-31    <--------
[309,] 326.80518 1.564260e+03
[310,] 327.61475 3.135520e-19

That's the mzXML:

Code: [Select]
<msRun scanCount="7098" startTime="PT2.0467S" endTime="PT1450.14S">
    <parentFile fileName="file://F://XXX.raw"
                fileType="RAWData"/>
    <dataProcessing centroided="1">
      <software type="conversion" name="ProteoWizard" version="2.2.3052"/>
      <processingOperation name="Conversion to mzML"/>
      <comment>Thermo/Xcalibur peak picking</comment>
    </dataProcessing>
    <dataProcessing>
      <software type="conversion" name="ProteoWizard" version="2.2.3052"/>
      <processingOperation name="Conversion to mzML"/>
    </dataProcessing>
...
    <scan num="419"
          scanType="FULL"
          centroided="1"
          msLevel="1"
          peaksCount="438"
          polarity="+"
          retentionTime="PT87.3367S"
          lowMz="40.262493133545"
          highMz="449.795928955078"
          basePeakMz="77.974868774414"
          basePeakIntensity="45256.39453125"
          totIonCurrent="3.933262835838e05">
--
IPB Halle                          Mass spectrometry & Bioinformatics
Dr. Steffen Neumann         http://www.IPB-Halle.DE
Weinberg 3 06120 Halle     Tel. +49 (0) 345 5582 - 1470
sneumann(at)IPB-Halle.DE
 

Re: mz sorting violation

Reply #2 –
ProteoWizard 3.0.3700 on Q-Exactive raw data, in Peak Picking (Prefer Vendor) mode, conversion to 64 bit mzML. The problem appears to be a mass stick which occurs twice. I tried with and without "remove zero samples" (since the offending data point was a zero-intensity point).

Re: mz sorting violation

Reply #3 –
Hi Paul

I have seen recently these error with data created on the a Waters mass spec converted to netcdf with databridge

Regards
Filippos

Re: mz sorting violation

Reply #4 –
Hi Paul,

I got that problem with databridge and samples were analysed on Q-Tof premier Waters instrument.

Thank you
Maggie

Re: mz sorting violation

Reply #5 –
Hi,

There is now an automatic fix in https://github.com/sneumann/xcms/tree/f ... assumption
which I'll pull into a Bioconductor version after the next release in April.

Yours,
Steffen
--
IPB Halle                          Mass spectrometry & Bioinformatics
Dr. Steffen Neumann         http://www.IPB-Halle.DE
Weinberg 3 06120 Halle     Tel. +49 (0) 345 5582 - 1470
sneumann(at)IPB-Halle.DE