Fragmentation Outcome Modelling: Prototype software for prediction of CID fragment ions for small molecule structures

MSMS of Midazolam, 1-OH Midazolam and 4-OH Midazolam gave 8, 11 and 10 fragment ions respectively. The fragmentation of each molecule was unique with each fragment ion being a unique mass. For comparative purposes the total number of fragment ions successfully predicted for each software package is expressed as a percentage of the total number of experimental fragment ions. Results are presented as per the above order: ACD Labs MS Manager (ESI mode) 75%, 46%, 70%; ACD Labs MS Manager (EI mode) 38%, 27%, 70%; Mass Frontier (ESI mode) 25%, 9%, 50%; Mass Frontier (EI mode) 38%, 36% 50%; Mass Fragment 63%, 55%, 80%; Fragmentation Outcome Modelling 100%, 100%, 100%. Fragmentation Outcome Modelling was the only application to successfully predict every fragment ion for each of the three examples given here. Typical processing time for each structure was less than one minute. There were marked differences between the capabilities of each respective software product tested and in general most packages were less successful with fragment ion predictions for the 1-OH and 4-OH metabolites.