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. On Thu, Dec 3, 2009 at 9:26 AM, Taejoon Kwon <[email protected]> wrote: > 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 [email protected] > [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 > > -- > > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
