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METLIN / Generation of theoretical fragment structures
I would be grateful if you could clarify a couple of points with respect to the Metlin functionality for the calculation and display of proposed fragment ion structures for MSMS data. I understand from a previous post in this area that you are using an implementation of the In Silico fragmentation methodology of Wolf et al described in BMC Bioinformatics 2010, 11:148.
1. Does the fragmentation prediction methodology work in real time as you (the user) access data via the MSMS function in Metlin or has someone populated each entry in the database manually?
2. How do I interpret the absence of structures for certain (coloured) peaks in the MSMS spectrum? Is it because the In Silico methodology cannot create a tangible structure or because that data has not been added to the database? There are a variety of 'success' rates for the predicted structures with many examples of almost complete coverage for all data in the MSMS spectrum, but there are other examples where few of the MSMS peaks have suggested structures.
3. Is there any way I can export the mass and relative intensity values for the MSMS data? I am a bit of a newbie to Metlin and perhaps I haven't discovered this functionality yet.
Thanks in Advance
Kirsten