Comparison of approaches for purifying and desalting polymerase chain reaction products prior to electrospray ionization mass spectrometry

We have compared the recovery and desalting efficiency of different methods (ethanol precipitation, dialysis/ultrafiltration, purification with commercial kits, anion-exchange chromatography) of purifying and desalting PCR products prior to analysis by high-resolution/high mass accuracy electrospray ionization mass spectrometry (LTQ-Orbitrap). The results support the use of anion-exchange chromatography, which shows excellent desalting efficiency with almost no adducts observed, along with a recovery of ∼70% and the ability to purify ∼10 samples in 45 min.