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
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