Hi Tomas, thanks for the info. I'm afraid I'm no coder, so I won't be able to help... Pity really as the software is very user friendly and very fast. I'm currently trying to work out to use OpenMS. I'm slowly getting there. It's powerful, but not user friendly at all.
Peter On Monday, 28 May 2012 11:47:37 AM, Tomas Pluskal wrote: > Hi Peter, > > >> 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. > > MZmine currently does not have any export feature to mzML nor MGF. > It can only export the peak list data to CSV or a primitive XML format. > >> 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? > > It is possible, if you write the module for MGF/mzML export :) > > >> 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? > > Currently such differences are not recognized. I agree it would be useful. > > > Best regards, > > Tomas > > > =============================================== > Tomáš Pluskal > G0 Cell Unit, Okinawa Institute of Science and Technology Graduate > University > 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan > TEL: +81-98-966-8684 > Fax: +81-98-966-2890 > ------------------------------------------------------------------------------ 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 [email protected] https://lists.sourceforge.net/lists/listinfo/mzmine-devel
