The delay in start up time for Agilent is a known issue. Unfortunately
the current Agilent API doesn't provide a way to get the list of scanIds
in a data file, nor a way to get a spectrum's scanId without getting its
data arrays. ProteoWizard is designed to support random access by
nativeID and by index to all of the data formats it supports, so it has
to enumerate all the spectra up front in order to get each of their
scanIds. On profile data, that takes a frustrating amount of time.
I have a feature request pending with Agilent to get a function which
provides either a list of scanIds or a spectrum without metadata.
Thanks for doing the comparison. I agree with Dave that the conversion
time sounds pretty long in both cases and I suspect a network share.
-Matt
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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