Dear Jimmy, the problem is that Thermo software is not especially intelligent by assigning the monoisotopic mass when a complex sample is analyzed. I actually would like to have the converter not making this decision. For that we have developed our own software. Can I somehow switch that option off for the acquisition ?
best Dominik On 08.09.2009, at 23:18, 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<herzog.ro...@googlemail.com> > 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 <domi...@ncbs.res.in> 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 743...@pqd21.00 [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" >>> >>> >QwwTJECWpu1DRCzTQI6UNkN9LWhACBJpQ4WhrkF77EZDhiVUQMXt9kOMqdFEmB26Q40 >>> pnEQ/DXdDk7vKQN3uzUOUOkRBDZl6Q5q4TkAD2xVD5iz9QXdOq0Pmu5ZBpkQSQ >>> +85U0LTIyND77R7QuHiLUP2vzNAAKBwRCUxu0CKXzZEJV9YQZWfu0Qu4S9AK0qJRDndh >>> EU/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 >>> domi...@ncbs.res.in >>> >> > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
