I have noticed the presence two mysterious peaks in almost every MS3 spectra acquired under RTS-SPS-MS3 mode on Eclipse.. These peaks are highlighted in the pic here.. I see them with both TMT and TMT Pro labels across different types of samples, and even with the Thermo Yeast TKO TMT Standard runs.. However, these peaks are not seen in TMT-MS2 acquisitions.. Have anyone else noticed this?? Any suggestion on where to start the investigation to uncover the mystery?? All leads are welcome.. Although those mysterious peaks are not impacting the outcome of the experiment, the mystery is kind of unsettling until it get resolved.. I am ready with my Sherlock hat on 😉
These peaks are most likely noise, created by respectively, the ion trap RF (~150) and the quad RF (at ~180). They would typically be eliminated from the displayed spectrum as exception peaks. There is a diagnostic “measure quad in Orbitrap” that would measure that frequency independently and update the exception list. Also exception peaks are typically hidden in QualBrowser/Freestyle, but can be viewed/hidden if this setting is changed.
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