That 742.5391 precursor mass is the monoisotopic m/z mass recorded in the scan header of the raw file itself. readw just grabs this value, if present, via the thermo interface. No way to turn this off in readw (besides a relatively simple edit of the code and rebuilding the binary).
Without seeing the data, it's impossible to confirm (or not) that the 742.5391 is actually wrong, especially compared to the filter line mass 743.54. But in a vast majority of the cases, the monoisotopic m/z mass, although not optimal, is much more accurate than the 2 decimal point filter line mass. On Mon, Sep 7, 2009 at 2:10 AM, Ronny<[email protected]> wrote: > > Hallo, > > I want to add something to the error described above: > > The correct precursor mass would be 743.54. A look into the MS/MS > spectrum of 744.55 reveals also a wrong precursor mass - namely > 742.5391. We think it might come from a kind of automatic isotopic > clustering. Is this done by readw or by the thermo-libraries? Is it > possible to switch this off? > > We would appriciate very much your help on that, since this incorrect > notion of precursor masses in the mzXML leads to wrong results in our > software. Writing a workaround on that would be very time consuming. > > thank you for your help and kind regards, > Ronny Herzog > > On Sep 6, 2:27 pm, Dominik Schwudke <[email protected]> wrote: >> Hallo, >> >> I have problem in the conversion of .raw files to mzXML with readw.exe. >> I have observed that in my complex samples wrong precusor masses are >> assigned. >> >> Here one example: >> >> <scan num="17" >> msLevel="2" >> peaksCount="20" >> polarity="-" >> scanType="Full" >> filterLine="ITMS - c NSI d Full ms2 [email protected] [50.00-755.00]" >> retentionTime="PT173.537S" >> lowMz="140.075" >> highMz="744.208" >> basePeakMz="743.461" >> basePeakIntensity="3062.26" >> totIonCurrent="5392.25" >> collisionEnergy="21" > >> <precursorMz precursorIntensity="518823" precursorCharge="1" >> activationMethod="PQD" >742.53875732</precursorMz> >> <peaks precision="32" >> byteOrder="network" >> contentType="m/z-int" >> compressionType="none" >> compressedLen="0" >> >QwwTJECWpu1DRCzTQI6UNkN9LWhACBJpQ4WhrkF77EZDhiVUQMXt9kOMqdFEmB26Q40pnEQ/DXdDk7vKQN3uzUOUOkRBDZl6Q5q4TkAD2xVD5iz9QXdOq0Pmu5ZBpkQSQ+85U0LTIyND77R7QuHiLUP2vzNAAKBwRCUxu0CKXzZEJV9YQZWfu0Qu4S9AK0qJRDndhEU/ZDpEOg1NQXUN1w==</peaks> >> </scan> >> >> Is somewhere a MS/MS grouping default set? How can I fix this error. >> >> best >> Dominiik >> >> -- >> Dr. Dominik Schwudke >> Group Leader >> >> National Centre for Biological Sciences >> Tata Institute of Fundamental Research >> GKVK, Bellary Road, >> Bangalore 560065, India >> >> Phone +91-80 – 23666499 >> [email protected] > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
