Dear Natalie, sorry for my last email. I had overseen that we have the wrong version again.
Thank You again. Natalie Tasman wrote: > Hello Dominik, Jimmy, > > Besides my recommendation to try msconvert, which is the program with > more developer focus at this point, there is already a command-line > option in the 4.3 series ReAdW program. I'd added this feature > because Thermo's software did not understand which scan to report for > the precursor mass for a rather complex user-defined method (in that > case, triggering from one mass and scanning at a different precursor > value.) > > From the usage statement: > > [Advanced option, default OFF] --precursorFromFilterLine: only > try to get the precursor MZ value from the Thermo > "filterline" text; only use this if you have a good reason! > Otherwise, the program first will try to obtain a more accurate > mass from the "Monoisotopic M/Z:" "trailer value" > > > -Natalie > > > > > > On Sep 8, 2009, at 11:09 AM, Dominik Schwudke wrote: > > >> 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<[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" >>>>> >>>>> >>>>>> 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 >>>>> [email protected] >>>>> >>>>> >> > > > > > -- 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 -~----------~----~----~----~------~----~------~--~---
