[spctools-discuss] Re: readw MS/MS precursor mass wrong
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 >>> 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 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: > > 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" > > activationMethod="PQD" >742.53875732 > byteOrder="network" > contentType="m/z-int" > compressionType="none" > compressedLen="0" > > >> QwwTJECWpu1DRCzTQI6UNkN9LWhACBJpQ4WhrkF77EZDhiVUQMXt9kOMqdFEmB26Q40 >> > pnEQ/DXdDk7vKQN3uzUOUOkRBDZl6Q5q4TkAD2xVD5iz9QXdOq0Pmu5ZBpkQSQ > + > 85U0LTIyND77R7QuHiLUP2vzNAAKBwRCUxu0CKXzZEJV9YQZWfu0Qu4S9AK0qJRDndh > EU/ZDpEOg1NQXUN1w== > > > 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 > > >> > > > > > -- 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,
[spctools-discuss] Re: readw MS/MS precursor mass wrong
Dear Natalie, Thank You for your detailed answer. I will look into msconvert. Im actually not sure about this part: > [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" > There is a command line option? But I have not seen it the help menu of readw. (readw.exe -h)! In our case the syntax would be "readw.exe -- precursorFromFilterline"; is that correct? How can I see the other advanced options? Thank you very much. best Dominik --~--~-~--~~~---~--~~ 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 -~--~~~~--~~--~--~---
[spctools-discuss] Re: readw MS/MS precursor mass wrong
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 >> 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 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: >>> 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" > >>> activationMethod="PQD" >742.53875732 >>> byteOrder="network" contentType="m/z-int" compressionType="none" compressedLen="0" > QwwTJECWpu1DRCzTQI6UNkN9LWhACBJpQ4WhrkF77EZDhiVUQMXt9kOMqdFEmB26Q40 pnEQ/DXdDk7vKQN3uzUOUOkRBDZl6Q5q4TkAD2xVD5iz9QXdOq0Pmu5ZBpkQSQ + 85U0LTIyND77R7QuHiLUP2vzNAAKBwRCUxu0CKXzZEJV9YQZWfu0Qu4S9AK0qJRDndh EU/ZDpEOg1NQXUN1w== 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 -~--~~~~--~~--~--~---
[spctools-discuss] Re: readw MS/MS precursor mass wrong
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 > 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 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: >>> >>> >> 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" > >>> >> activationMethod="PQD" >742.53875732 >>> >> byteOrder="network" >>> contentType="m/z-int" >>> compressionType="none" >>> compressedLen="0" >>> >>> >QwwTJECWpu1DRCzTQI6UNkN9LWhACBJpQ4WhrkF77EZDhiVUQMXt9kOMqdFEmB26Q40 >>> pnEQ/DXdDk7vKQN3uzUOUOkRBDZl6Q5q4TkAD2xVD5iz9QXdOq0Pmu5ZBpkQSQ >>> +85U0LTIyND77R7QuHiLUP2vzNAAKBwRCUxu0CKXzZEJV9YQZWfu0Qu4S9AK0qJRDndh >>> EU/ZDpEOg1NQXUN1w== >>> >>> >>> 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 -~--~~~~--~~--~--~---
[spctools-discuss] Re: readw MS/MS precursor mass wrong
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 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 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: >>> >>> >> 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" > >>> >> activationMethod="PQD" >742.53875732 >>> >> byteOrder="network" >>> contentType="m/z-int" >>> compressionType="none" >>> compressedLen="0" >>> >>> >QwwTJECWpu1DRCzTQI6UNkN9LWhACBJpQ4WhrkF77EZDhiVUQMXt9kOMqdFEmB26Q40pnEQ/DXdDk7vKQN3uzUOUOkRBDZl6Q5q4TkAD2xVD5iz9QXdOq0Pmu5ZBpkQSQ+85U0LTIyND77R7QuHiLUP2vzNAAKBwRCUxu0CKXzZEJV9YQZWfu0Qu4S9AK0qJRDndhEU/ZDpEOg1NQXUN1w== >>> >>> >>> 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 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 -~--~~~~--~~--~--~---
[spctools-discuss] Re: readw MS/MS precursor mass wrong
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 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 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: >> >> > 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" > >> > activationMethod="PQD" >742.53875732 >> > byteOrder="network" >> contentType="m/z-int" >> compressionType="none" >> compressedLen="0" >> >QwwTJECWpu1DRCzTQI6UNkN9LWhACBJpQ4WhrkF77EZDhiVUQMXt9kOMqdFEmB26Q40pnEQ/DXdDk7vKQN3uzUOUOkRBDZl6Q5q4TkAD2xVD5iz9QXdOq0Pmu5ZBpkQSQ+85U0LTIyND77R7QuHiLUP2vzNAAKBwRCUxu0CKXzZEJV9YQZWfu0Qu4S9AK0qJRDndhEU/ZDpEOg1NQXUN1w== >> >> >> 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 -~--~~~~--~~--~--~---
[spctools-discuss] Re: readw MS/MS precursor mass wrong
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 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: > > 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" > > activationMethod="PQD" >742.53875732 > byteOrder="network" > contentType="m/z-int" > compressionType="none" > compressedLen="0" > >QwwTJECWpu1DRCzTQI6UNkN9LWhACBJpQ4WhrkF77EZDhiVUQMXt9kOMqdFEmB26Q40pnEQ/DXdDk7vKQN3uzUOUOkRBDZl6Q5q4TkAD2xVD5iz9QXdOq0Pmu5ZBpkQSQ+85U0LTIyND77R7QuHiLUP2vzNAAKBwRCUxu0CKXzZEJV9YQZWfu0Qu4S9AK0qJRDndhEU/ZDpEOg1NQXUN1w== > > > 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 -~--~~~~--~~--~--~---
