Spectra in PCD


I want to import spectra in my PCD (just formula and mass included). I first ran my compound in targeted MSMS mode. Then I performed a Qual analysis (workflow: compound discovery,  find by targeted MSMS). I exported the spectra as .cef file and then I added them to my PCD. The spectra don't look good though. There is a lot of noise and unknowns. Then I tried to run a find by molecular feature in Qual so that I can get the peak annotations but it seems that it identifies more than a thousand of compounds! In general, I am wondering what is the exact procedure if someone wants to add his own spectra in a PCD. Is  there any technical note or something that describes in very detail the workflow to be followed.

Thank you in advance


  • Hello  ,

    There is some good general information about acquiring and extracting spectrum from qual for PCDLs in the PCDL Quick Start Guide. You can find a copy for your version on the installation media or there is a copy available from the agilent.com website.

    PCDL Quickstart

    Page 71 is a good place to start for this process. 

    Finding the best settings for any of the Find By algorithms will be very dependent on your data and take time and patience. If you are finding too many compounds start by raising the area or height filtering significantly and then work back down to find an appropriate value. The method settings are applied from left to right through the settings tabs, so try starting by increasing the peak filter in the first tab so that the following steps aren't overwhelmed with too many results. Then just keep working from there. 

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