The replacement of acetonitrile with methanol for PAH analysis has had several problems:
1) there is a tendency for PAH extracts from animal tissues to precipitate, meanings that we have to often, refilter several samples
2) backpressure is often in excess of 3000 PSI
3) we can separate the key carcinogenic PAHs that are part of risk assessment protocols but many common PAHs such as phenanthrene are not cleanly separated. Similarly, indeno is not well resolved either.

At the moment, I’m running my samples under this method but hopefully the acetonitrile shortage will end and will switch back to acetonitrile. However, varian has provided me with a link that has a lot of detail about switching solvents.

http://www.varianinc.com/cgi-bin/nav?/products/techtip/0509/index

Hope this helps