precursor_mz in mzXML

[Taejoon Kwon]

Hi,

I converted my RAW file with ReAdW 4.3.1, and found some strange
inconsistency in precursor m/z.

----
<scan num="1333"
msLevel="2"
peaksCount="656"
polarity="+"
scanType="Full"
filterLine="ITMS + c NSI d Full ms2 672...@cid35.00
[175.00-2000.00]"
retentionTime="PT2387.37S"
lowMz="191.012"
highMz="1982.6"
basePeakMz="823.611"
basePeakIntensity="1722.97"
totIonCurrent="13151.2"
collisionEnergy="35" >
<precursorMz precursorIntensity="0" precursorCharge="4"
activationMethod="CID" >672.3157959</precursorMz>
----

In filterLine, ms2 precursor m/z is recorded as '672.57'. However, in
precursorMz element, it is said as '672.3157959'. It is not only for
the m/z value, but also for precursorIntensity. I looked at ms1
spectra, and found the strong peak near 672.57, not near 672.315.

I wonder how precursorMz is converted in ReAdW, and any reason of this
inconsistency.

For your information, here is the header of converted mzXML.

----
<?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="14565" startTime="PT0.5709S" endTime="PT17999.6S" >
<parentFile fileName="MSups_5ul.RAW" fileType="RAWData"
fileSha1="963090b48d2ce691f80b3309c7d90f86680be450" />
<msInstrument>
<msManufacturer category="msManufacturer" value="Thermo
Scientific" />
<msModel category="msModel" value="LTQ Orbitrap" />
<msIonisation category="msIonisation" value="NSI" />
<msMassAnalyzer category="msMassAnalyzer" value="FTMS" />
<msDetector category="msDetector" value="unknown" />
<software type="acquisition" name="Xcalibur" version="2.4 SP1" />
</msInstrument>
<dataProcessing>
<software type="conversion" name="ReAdW" version="4.3.1(build Sep
9 2009 12:30:29)" />
</dataProcessing>
-----

Thanks,

Taejoon Kwon

[Jimmy Eng]

The 672.3157959 mass is likely from the scan header in the raw file
for that particular scan. Open up the raw file in qualbrowser and
take a look at the scan header and see what the "monoisotopic m/z"
value is. (Hopefully it's 672.3157959).

This would just explain the discrepancy. Why the m/z values are so
far apart between the filter line and the mono isotopic m/z value is a
question for whomever acquired the data or for Thermo.

> --
>
> You received this message because you are subscribed to the Google Groups "spctools-discuss" group.
> To post to this group, send email to spctools...@googlegroups.com.
> To unsubscribe from this group, send email to spctools-discu...@googlegroups.com.
> For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
>
>
>

[Matthew Chambers]

672.315 is the monoisotopic m/z that the instrument reported. It's not
the most intense peak because it's a +4 ion: it's expected that the +1
isotope is the most intense.

-Matt

[Taejoon Kwon]

Thank you, Jimmy and Matt. Does this discrepancy affect zero
'precursorIntensity' also?

Taejoon

On Dec 3, 11:38 am, Matthew Chambers <matthew.chamb...@vanderbilt.edu>
wrote:

> > mzXML_3.1http://sashimi.sourceforge.net/schema_revision/mzXML_3.1/mzXML_idx_3...."