Dear group,
While trying to search files obtained upon conversion of Agilent
QTOF .d files to mzXML with msconvert, I realized that the .dta files
created for Sequest search were very few and had a very strange
numbering.
(Windows XP, msconvert version tried: Build_12_ProteoWizard_r2127 or
pwiz-bin-windows-x86-vc90-1_6_1386 or pwiz-bin-windows-x86-vc90-
release-shared-2_1_2485).
Upon investigating a bit, it seems that msconvert performs a wrong
numbering of the scans from the .d files.
Here is an example of the 2 first scans obtained from an mzXML files
from msconvert:
-----msconvert---------
<scan num="2567"
scanType="FULL"
centroided="1"
msLevel="1"
peaksCount="428"
polarity="+"
retentionTime="PT2.56S"
basePeakIntensity="179"
totIonCurrent="26996"
msInstrumentID="IC1">
<peaks compressedLen="0"
precision="32"
byteOrder="network"
pairOrder="m/z-int">Q5PZKkCAzM1DlQ...</peaks>
</scan>
<scan num="3560"
scanType="FULL"
centroided="1"
msLevel="1"
peaksCount="422"
polarity="+"
retentionTime="PT3.553S"
basePeakIntensity="282"
totIonCurrent="26252"
msInstrumentID="IC1">
<peaks compressedLen="0"
precision="32"
byteOrder="network"
pairOrder="m/z-int">Q5QsjkEmAABDlKV/...</peaks>
</scan>
----------------------
Here is the same 2 first scans from the trapper conversion
-------trapper converter-------
<scan num="1"
msLevel="1"
peaksCount="428"
polarity="+"
scanType="MS1SurveyScan"
retentionTime="PT2.56S"
lowMz="295.697"
highMz="1953.19"
basePeakMz="1222"
basePeakIntensity="183.267"
totIonCurrent="26996" >
<nativeScanRef coordinateType="Agilent" >
<coordinate name="scan"
value="2567" />
</nativeScanRef>
<peaks precision="32"
byteOrder="network"
contentType="m/z-int"
compressionType="none"
compressedLen="0" >Q5PZKkCAzM1DlQsCQgn...</peaks>
</scan>
<scan num="2"
msLevel="1"
peaksCount="422"
polarity="+"
scanType="MS1SurveyScan"
retentionTime="PT3.553S"
lowMz="296.348"
highMz="1965.69"
basePeakMz="391.288"
basePeakIntensity="283.565"
totIonCurrent="26252" >
<nativeScanRef coordinateType="Agilent" >
<coordinate name="scan"
value="3560" />
</nativeScanRef>
<peaks precision="32"
byteOrder="network"
contentType="m/z-int"
compressionType="none"
compressedLen="0" >Q5QsjkEmAABDlKV/Qb...</peaks>
</scan>
-------------------
As you may realize, the scan numbers from the msconver conversion are
actually, for whatever reason, the time in milli-seconds?!? (e.g. scan
1 <=> 2.56sec <=> scan num="2567" !!!!!)
So here are my questions:
1) is there a script (I think there is but I cannot put hands on it
anymore) among the TPP executables to renumber the scans
consecutively?
2) Could you release a fix for this Agilent file conversion in a
future msconvert release?
Thanks in advance for you inputs,
Best,
Ludovic
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