IDEOM and 'multiple negative scan events'

[Lucas Schwartzenberg]

Is the a way to 'covert RAW to mzXML' on RAWs that contain multiple negative polarity mode scans?

We were having problems with an interfering substance (at 93. ) in our negative polarity mode scans, which was causing our real signals to get lost in the noise. So it was decided to work around the issue by splitting the the scan into two parts, to omit the signal between 93.0 and 93.5.
But the raw-file converter doesn't seem to pick up on the third scan mode (one positive and two negative), and cannot find any peaks.

Is there a way to convert (and then process) data from both negative polarity mode scans, onto one or more peakML files?
If not, can I force the converter to use one particular of the two negative polarity mode scans, depending on which mass-range has the more interesting content?

Rgui outputs:

Converting RAWs:

Type 'q()' to quit R.

> setwd("C:/Users/3125319/Desktop/EZ20140612")
> converter <- c("C:/Program_Files/ProteoWizard/ProteoWizard_3.0.6090/msconvert.exe")
> FILES <- list.files(recursive=TRUE,full.names=TRUE,pattern="\\.raw")
> for (i in 1:length(FILES)){system (paste(converter," --mzXML --32 --filter \"peakPicking true 1\" --filter \"polarity positive\" -o Positive -v",FILES[i]))}
format: mzXML
    m/z: Compression-None, 32-bit
    intensity: Compression-None, 32-bit
    rt: Compression-None, 32-bit
ByteOrder_LittleEndian
 indexed="true"
outputPath: Positive
extension: .mzXML
contactFilename:

filters:
  peakPicking true 1
  polarity positive
 
filenames:
  .\QC_01.raw
 
processing file: .\QC_01.raw
writing output file: Positive\QC_01.mzXML
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format: mzXML
    m/z: Compression-None, 32-bit
    intensity: Compression-None, 32-bit
    rt: Compression-None, 32-bit
ByteOrder_LittleEndian
 indexed="true"
outputPath: Positive
extension: .mzXML
contactFilename:

filters:
  peakPicking true 1
  polarity positive
 
filenames:
  .\QC_02.raw
 
processing file: .\QC_02.raw
writing output file: Positive\QC_02.mzXML
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format: mzXML
    m/z: Compression-None, 32-bit
    intensity: Compression-None, 32-bit
    rt: Compression-None, 32-bit
ByteOrder_LittleEndian
 indexed="true"
outputPath: Positive
extension: .mzXML
contactFilename:

filters:
  peakPicking true 1
  polarity positive
 
filenames:
  .\QC_03.raw
 
processing file: .\QC_03.raw
writing output file: Positive\QC_03.mzXML
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format: mzXML
    m/z: Compression-None, 32-bit
    intensity: Compression-None, 32-bit
    rt: Compression-None, 32-bit
ByteOrder_LittleEndian
 indexed="true"
outputPath: Positive
extension: .mzXML
contactFilename:

filters:
  peakPicking true 1
  polarity positive
 
filenames:
  .\QC_04.raw
 
processing file: .\QC_04.raw
writing output file: Positive\QC_04.mzXML
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> for (i in 1:length(FILES)){system (paste(converter," --mzXML --32 --filter \"peakPicking true 1\" --filter \"polarity negative\" -o Negative -v",FILES[i]))}
format: mzXML
    m/z: Compression-None, 32-bit
    intensity: Compression-None, 32-bit
    rt: Compression-None, 32-bit
ByteOrder_LittleEndian
 indexed="true"
outputPath: Negative
extension: .mzXML
contactFilename:

filters:
  peakPicking true 1
  polarity negative
 
filenames:
  .\QC_01.raw
 
processing file: .\QC_01.raw
writing output file: Negative\QC_01.mzXML
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format: mzXML
    m/z: Compression-None, 32-bit
    intensity: Compression-None, 32-bit
    rt: Compression-None, 32-bit
ByteOrder_LittleEndian
 indexed="true"
outputPath: Negative
extension: .mzXML
contactFilename:

filters:
  peakPicking true 1
  polarity negative
 
filenames:
  .\QC_02.raw
 
processing file: .\QC_02.raw
writing output file: Negative\QC_02.mzXML
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format: mzXML
    m/z: Compression-None, 32-bit
    intensity: Compression-None, 32-bit
    rt: Compression-None, 32-bit
ByteOrder_LittleEndian
 indexed="true"
outputPath: Negative
extension: .mzXML
contactFilename:

filters:
  peakPicking true 1
  polarity negative
 
filenames:
  .\QC_03.raw
 
processing file: .\QC_03.raw
writing output file: Negative\QC_03.mzXML
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format: mzXML
    m/z: Compression-None, 32-bit
    intensity: Compression-None, 32-bit
    rt: Compression-None, 32-bit
ByteOrder_LittleEndian
 indexed="true"
outputPath: Negative
extension: .mzXML
contactFilename:

filters:
  peakPicking true 1
  polarity negative
 
filenames:
  .\QC_04.raw
 
processing file: .\QC_04.raw
writing output file: Negative\QC_04.mzXML
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>()q



Running XCMS:
> for (i in 1:length(rawfiles)){xset <- xcmsSet(rawfiles[i], method='centWave', ppm=2, peakwidth=c(5,100), snthresh=3, prefilter=c(3,1000), integrate=1, mzdiff=0.001, verbose.columns=TRUE, fitgauss=FALSE, nSlaves=1)
+ PeakML.xcms.write.SingleMeasurement (xset=xset,filename=outputfiles[i],ionisation="negative",addscans=2,writeRejected=FALSE,ApodisationFilter=TRUE)}

 Detecting mass traces at 2 ppm ...
 % finished: 0 10 20 30 40 50 60 70 80 90 100
 0 m/z ROI's.
No ROIs found !
negative
retrieving raw data
- C:/Users/3125319/Desktop/EZ20140612/Negative/./QC_01.mzXML
Error in xset@peaks[peakid, ] : subscript out of bounds
In addition: Warning messages:
1: In .local(object, ...) :
  It looks like this file is in profile mode. centWave can process only centroid mode data !

2: No peaks found in sample QC_01