Hi,
This seems like a *really* long time for both tools even if the file
contains a lot of scans. Are you converting files over a slow network
share or similar?
We regularly convert Agilent 6520 QTOF files to mzXML using trapper and
msconvert. For trapper it takes about 27s to convert a file with 8800
scans to mzXML using centroid mode, or 8m 20s for profile mode.
These timings are on a server with Xeon 5550s and 16GB of RAM, but I
wouldn't expect conversions to take hours, even on my 2 yr old laptop.
msconvert is usually about twice as slow as trapper when converting
using 32-bit precision.
DT
On 16/02/2010 20:52, bio.x2y wrote:
Hi,
I independently used both Trapper (4.3.1) and Msconvert (pwiz 1.6.0)
to convert a 1.4Gb Agilent MassHunter ".d" file containing ~16000
spectra to mzXML.
Parameters:
$msconvert --mzXML --verbose large.d
$trapper --mzXML -v large.d large.mzXML
Msconvert took 5hrs 38mins to complete, generating a 57Gb file.
Trapper took 1hr 26mins to complete, generating a 28Gb file.
I can understand the differences in size, given the differences in
structure and precision. However, the time difference still appears
quite high.
One interesting observation is that msconvert does not start writing
to the output file until 1hr 20min has elapsed. At that point, the
file begins filling and the progress messages start appearing in the
output. Trapper, on the other hand, starts filling the output file and
reporting progress immediately.
I have seen this occur now for two runs on two different days, so I
don't think it's related to other activity on the machine.
Perhaps msconvert is engaging in some preprocessing that isn't
strictly necessary, for Agilent ".d" files at least?
Thanks,
bio.x2y
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