I've mentioned Picky on this blog before, but I don't think it's possible to bring enough exposure to some tools and Picky is definitely one of them.
You can read about it at Nature methods here.
But that's probably not what you actually want to do. What you actually want to do is go here:
And use this awesome Shiny app to just build your method of choice. Look, you can build your own awesome PRM or SRM targeted experiment. You can think really hard about cycle time on your D30 vs your D20 system or flip a coin to decide whether you should use static dwell time or set a maximum cycle on your newest triple quads. Or...you can focus on your experimental design and data output and just design your targeted experiment with....
The clip I took from the one I'm building is chosen because I need to target an alternative sequence isoform. Which I could definitely do this morning -- OR -- I could just press the button on Picky.....
...and magically open the door to selective targeting of Proteoforms!
All jokes aside, if there is an easier way in this world of dealing with targeting alternative protein isoforms, send me an email so I start using it!