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]
>>>>
>>>
>>
>>>
>
>
> >
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