Yeah, I'd like to see the isolation window from the triggering survey scan because it seems unlikely that the monoisotopic m/z would be less accurate than the filter's isolation m/z (except it might pick the a+1 peak, but that's almost certainly still better than the isolation m/z).
-Matt Jimmy Eng wrote: > 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 --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
