How can I use MSMS or MSᴱ information to improve my compound identifications?
Progenesis QI allows you to search for compound identifications based not only on compound properties such as neutral mass, retention time and CCS (the latter two with the MetaScope search method), but also on the fragmentation patterns produced by compounds in your experiment.
There are 3 options on how to handle fragmentation data in your experiment:
- Do not use fragmentation data
- Any fragmentation data in your experiment will be ignored.
- Perform theoretical fragmentation
- Your experimental fragmentation data is compared to theoretical fragmentation patterns generated by the simulated breaking of bonds in the structures of possible identifications. You can choose this option when using the MetaScope and ChemSpider search methods.
- Perform fragment database search
- Your experimental fragmentation data is compared to known fragmentation patterns of a library of compounds, which are stored in a fragment database. The LipidBlast and NIST MS/MS Library search methods each use a fragment database specific to them and with MetaScope, you can use your own.
After performing the search, you’ll be presented with a fragmentation score where a high score represents a high number of peak / observed fragment matches.