importing ms/ms data using dacserver.dll

<p>Hello,</p><p></p><p>I wrote code (C++ in Visual Studio on Windows 7) that imports data from raw MS files using the dacserver.dll.  We are going to start collecting ms/ms data.  I am not familiar with the structural differences between MS and MS/MS data, so I read "MassLynx 4.1 Interfacing Guide" which touches on the subject in section 7, the "Datafile Access Component" chapter.  Specifically, I (assume) that I need to know which spectra are ms/ms spectra and how to import the dwell time, and anything else useful. </p><p></p><p>Thank you,</p><p></p><p>Katherine</p>


  • Hello Katherine

    A nice beginning to understanding what MS/MS data can be read at the link

    So to summarize, MS/MS is the combination of two or more MS experiments.

    The aim is either to get structure information by fragmenting the ions isolated during the first experiment, and/or to achieve better selectivity and sensitivity for quantitative analysis.

    MS/MS is done:

    • either by coupling multiple analyzers (of the same or different kind)

    • or, with an ion trap, by doing the various experiments within the trap

    There are four main scan experiments possible using MS/MS (which are all different from the regular Single Ion Recording or MS Scan data of MS only experiments)

    Precursor ion scan

    The product ion is selected in the second mass analyzer, and the precursor masses are scanned in the first mass analyzer. A precursor ion scan cannot be done with time based MS instruments. Note that precursor ion[2] is synonymous with parent ion[3] and product ion[4] with daughter ion;[5] however the use of these anthropomorphic terms is discouraged.[6][7]

    Product ion scan

    A precursor ion is selected in the first stage, allowed to fragment and then all resultant masses are scanned in the second mass analyzer and detected in the detector that is positioned after the second mass analyzer. This experiment is commonly performed to identify transitions used for quantification by tandem MS.

    Neutral loss scan

    The first mass analyzer scans all the masses. The second mass analyzer also scans, but at a set offset from the first mass analyzer.[8] This offset corresponds to a neutral loss that is commonly observed fo...

  • Dot,

    I really appreciate the information about MS/MS data.  The links are helpful too.  Your explanation and the links to other info, taken together, are great.

    On to my programming question -- I wrote a DLL in C++ that imports spectral data from Waters raw files.  My code currently imports the DACServer.dll file, and creates a IDACSpectrumPtr object.  My code then pulls masses and intensities by calling the GetSpectrum function.  So, my question is how do I get MS/MS specific data from this object?  I am importing MS/MS scans, but no distinction is made upon import, using my code, of whether each individual spectrum is MS or MS/MS.  I'd also like to pull the dwell times out, when available, and any other MS/MS related data that may be available in a Waters raw file.

    Thank you very much for your help.


  • Is there no one who can answer programming questions?  Did I post this in the wrong community?



  • Hmmmm...not sure what to do next.  Is there no one with a suggestion?   Thanks, Katherine

  • Hi Katherine,

    There is no way to determine the data type from the DACSpectrum object, as you have found, it just has mass-intensity information. Getting at the data type may require you signing a non-disclosure agreement (NDA) with Waters. I will ask around internally to see if there is another DAC object you can use to obtain data type information.

    Regards, Paul.

  • Thank you for your answer.  I appreciate your help with this.  If I don't hear from you again, I will assume this information is currently proprietary.



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