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However, with the MultiNotch MS3 method we employ multiple isolation notches, and some of those notches tend to be larger than the isolation notches of the standard MS3 method (see Methods); hence, we lose some selectivity with the MultiNotch method compared to the standard.
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At the same time, we maintain the selectivity of the standard MS3 method by carefully defining the isolation notches of the SPS isolation waveform to ensure high isolation specificity of the target MS2 fragment ions.
As the q-value of the ion varies, so does the optimal position and width of the isolation notch.
This method also captures multiple MS2 fragment ions in the MS3 precursor population using isolation waveforms with multiple frequency notches (i.e., synchronous precursor selection).
Using isolation waveforms with multiple frequency notches, we coisolated and cofragmented multiple MS2 fragment ions during our MS3 analyses (MultiNotch MS3).
Herein, we describe a solution to the sensitivity limitations of the MS3 method, in which we use isolation waveforms with multiple frequency notches for synchronous precursor selection (SPS) of multiple MS2 fragment ions.
Using isolation waveforms with multiple frequency notches (i.e., synchronous precursor selection, SPS), we coisolated and cofragmented multiple MS2 fragment ions, thereby increasing the number of reporter ions in the MS3 spectrum 10-fold over the standard MS3 method (i.e., MultiNotch MS3).
The idea of concurrently isolating multiple discrete ion populations with isolation waveforms that have multiple frequency notches was developed in the mid-1980s, when much of the original work was done in the laboratories of Marshall and McLafferty.
To address these impacts, multiple notches were cut through the constructed foredune.
This type of noise can be attenuated by a filter with multiple notches [12].
Hence, the model simplifies the Swiss scheme, which contains multiple notches (see Fig. 1).
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