Hi, I'm trying to find a good way for doing MS2 peak detection from mzML files and saving the peaklists in MGF. I'd be happy if I can save as an mzML and then convert using PWiz (for example). I've worked out how to use mzMine (2.8) to detect MS2 peaks. What I can't figure out is how to export the resulting peak lists in a convenient, ie. batch, method. I want to use the generated MGFs for submission into multiple search algorithms.
What I'd like to be able to do is load numerous files via the batch process menu, do the peak finding and export the resulting MS2 list. Is this possible? While I'm here, is it possible to use different peak setting parameters for different activation types? The data is collected using an LTQ-Orbitrap. As such, I can collect CID and/or HCD data. The CID is collected in the LIT, so it's low res and the HCD is recorded in the Orbi, so it's high res. Both types of data can be collected in the same LC-MS/MS run. Can mzMine cope with this and process the data appropriately? Thanks again, Peter ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
