IE-Omics is a R script that automates “iterative exclusion” (IE) experiments for Thermo instruments. This script can easily be modified for use with other instruments. IE-Omics applies Iterative exclusion to traditional data-dependent tandem mass spectrometry top N experiments (ddMS2-topN), where the N most intense ions detected in a full scan are selected for fragmentation. In IE, previously selected ions for fragmentation using ddMS2-topN are excluded from selection in sequential injections. Theoretically fragmentation of all ions above a certain intensity threshold can be acquired. Applying this technique in our laboratory to Red Cross plasma and substantia nigra, we were able to identify up to 69 % more lipids than using traditional data-dependent acquisition.

Jeremy P. Koelmel, Nicholas M. Kroeger, Emily L. Gill, Candice Z. Ulmer, John A. Bowden, Rainey E. Patterson, Richard A. Yost, Timothy J. Garrett: Expanding lipidome coverage using LC-MS/MS data-dependent acquisition with automated exclusion list generation. Journal of the American Society for Mass Spectrometry. (2017) 28: 908. doi:10.1007/s13361-017-1608-0