In short: it depends on the structure of your compound. If your compound has heteroatoms easily ionizable then ESI work well (nucleic acids, proteins, organic acids or amines etc.); if you have neutral polymers, steroids, aromatic compounds without polarizable groups then you have better chances with APCI; if you have condensed aromatic rings (graphenes, PAHs etc.) then APPI is the better choice. But it also depend on which device you have access to, and on the working flow, since APCI and APPI usually are used at 0.2-1 mL/min while you can work in ESI at 4-6 uL/min. take a look at

http://www.google.it/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&cad=rja&uact=8&ved=0CE0QFjAC&url=http%3A%2F%2Fwww.asms.org%2Fdocs%2Fconference-short-slides%2Flc_ms_voyksner.pdf%3Fsfvrsn%3D2&ei=_Mo7U9eGJIPsywP8v4GIAw&usg=AFQjCNGYFWpNmju1zuRL_srsMaPP2pcy-A&sig2=vuJB0TvlHzZhY3PcZ63kqA&bvm=bv.63934634,d.bGQ