I love SRM. Hell, everyone loves SRMs. Nothing beats getting your ion of interest and identifying it with 1) retention time 2) mass, and 3) fragment ion(s). The problem is that they are sloooooowwww to set up because method optimization is such a drag. You've got to find the right fragment ion and collision energy to make it show up at the highest efficiency (if someone hasn't done it for you -- on your particular instrument, of course). It isn't such an issue in proteomics, but in small molecule work SRM collision energies for particular compounds can be the biggest secrets in the world.
That's why this paper in MCP lab from Amelia Pierson et al., of the Koon lab is so cool!
Parallel reaction monitoring uses the targeted multiplex MS2 method on the Q Exactive and essentially lets you get a bunch of SRMs (or MRMs, depending on what you're calling it) all at the same time. Not only is it faster, but because the Q Exactive has an inclusion list of up to 5,000 ions all selectable by retention time, with the right chromatography system you can validate hundreds of observations in one go. MS based virtual western blots in realistic time may actually be a reality!
There are some huge advantages here --
1) You are getting high resolution fragments!
2) You are getting a lot of them (all of them?) at once so you can be selective in processing (if you've got a co-eluting compound of striking similarity, you can ignore that fragment ion and focus on ones that are truly unique
3) Less up front setup time!
EDIT: Holy cow. This post was live for 7 years with a really awful typo in it. Thank you to any person who ever saw this and ever talked to me or took me serious about anything in regards to mass spectrometry ever again. Fixed....