A well constructed mzXML file would normally be somewhat smaller than
its mzML equivalent - make sure you've got peaklist compression turned
on (IIRC the msconvert default is no compression, which seems like a
Bad Thing to me but there you have it).
On Wed, Mar 2, 2011 at 10:37 PM, ben
I haven't played around with compression, but that would be simply
adding a -z [ --zlib ] correct? I am using this page more so than
the help on sourceforge for command arguments.
http://groups.google.com/group/xcms/msg/53e2a2b462a5448c
Thanks for the help, and I will let you know if something
If you want to post some samples to the list, use msconvert with an index
filter. Try:
msconvert original.mzML -o subset --filter index 0-100 -z
msconvert original.mzML -o subset --filter index 0-100 -z --mzXML
And attach both the subset mzML and mzXML for comparison.
Thanks,
-Matt
On
I wanted to provide an update. First, it appears that the export mgf
function from within peak view isn't very good and talking to AB folks
it seems more like a left over beta function. Second, the AB folks
have unanimously confirmed that the mascot.dlll script shouldn't be
used in this case
Hi Ben,
I do not know how you look at your runs, but the PeakView software (I
use Version 1.1) that open the raw data wiff files can actually export
mgf format.
You need to open the IDA runs with the IDA explorer, select filtering
criteria you want (rt, spectra quality) and then right click on the
I didn't realize that about PeakView. So I am generating mgfs from a
single wiff 4 ways right now: dll script within Analyst, dll script
within Daemon, through PeakView (which took about two seconds), and
using Distiller (going on 3 hours right now). Then I will compare
them.
Thanks for all the
