Pitchers, however, are valued very differently by the different systems. FIP is a linear weights based system that treats all balls in play as equally valuable and ignores sequencing. Baseball-Reference starts with runs allowed and works backwards. Baseball Prospectus uses a complex modeling system to attempt to derive the value of individual events while controlling for contextual factors. You have to decide which method is the one you prefer, although looking at each site is the best way to get a complete picture of the player.
Piper Slowinski, March 22, 2012, FanGraphs dot com
It continues to be excellent advice, in particular for pitchers.