How to set an MS2 Scan method in Triple Quad 6460 to get proper MS2 scan spectra

Hello MS scientist, 

I am facing a problem to set an MS2 Scan method in Triple Quad 6460 instrument. I am trying to analyze caffeine at the MS2 level but I am not getting a proper MS2 scan peak. 

Please guide me with the proper method.  

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  • Are you just seeing noise? You have quite a large injection volume - what is the concentration? What are the mobile phases you are using?

    I would also set the Sheath Gas Temp to 400oC and the Drying Gas Temp to 200oC and try again. The other parameters will need optimizing once you have your MRM setup.

  • Hi, 

    Thank you for your suggestions. Concentration- 100ug/ml, 15ul injection volume, Mobile phase- A-0.1% FA in water, B-0.1% FA in 100% methanol. 

    Please find the Mass Hunter Quantitative software image. This image is showing just the MS spectrum.  

  • So you have a peak in the TIC at approx 14.5 minutes. What does the spectrum look like? Can you share the peak apex spectrum? The monoisotopic mass of caffeine when protonated (M+H+) is 195.1m/z but the molecule can fragment to give a product ion with a monoisotopic mass of 138.1m/z. You should look for those two masses in the spectrum. Anyway it looks like you may have your caffeine peak there - good news Smiley. Caffeine is relatively polar - on our Eclipse Plus C18 columns it typically elutes at approx 10-15% Acetonitrile. If you want an earlier elution time, simply increase the percentage of methanol you are delivering from the pump or shorten the gradient time - its not clear if you are using an isocratic or gradient method. 

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