Thanks for your post. We did an experiment like this back in 2010 (
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2813958/). This method gave some interesting results in terms of the number of peptides that could be qualitatively detected in a run. I believe that Skyline should be able to analyze data collected in this way but it would require you to come up with how you are going to shift the m/z range over time and acquire the data.
That said we haven't done much with this in recent years because we felt an advantage of DIA over PRM was the simplicity and generalization of a data acquisition method to most samples. Once we get into scheduling the RT we have to come up with strategies to shift the location of the isolation windows pending any RT shift between runs. If we don't then we face potentially losing peptides in some runs but not others because they fall in and out of the isolation range at a given time.
Our priorities have been less about increasing the number of peptides that can be detected in a run and more about improving the quantitative capabilities across many runs. It would be great if shifting the location of the isolation windows improved both.
Let us know how your experiments work.
Mike