Generation of theoretical fragment structures March 08, 2013, 08:38:36 AM HiI 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 AdvanceKirsten Quote Selected
Re: Generation of theoretical fragment structures Reply #1 – March 11, 2013, 05:43:32 PM Hi Kirsten,1. We update the fragmentation prediction once every a couple of week, so yes it's manually updated.2. Some of the peaks, we can't generate the predicted structure due to the rearrangement or we do not have enough information to predict the suitable fragments.3. We do not offer downloadable MSMS data, but we do offer SOAP service where you can query METLIN's tandem MS data based on your data.Thanks for using METLIN -Kevin Quote Selected
Topic: Generation of theoretical fragment structures