Hi Thomas,
lol wut?
ProteoWizard release: 3.0.3916 (2012-8-27)
ProteoWizard MSData: 3.0.3898 (2012-8-22)
msbenchmark spectra binary c:\test\B06-11071.mzXML
Enumerating spectra: 6687/6687 (78477534 data points)
Time elapsed: 00:00:19.681968
msbenchmark spectra binary c:\test\B06-11071.mzXML
Enumerating spectra: 6687/6687 (78477534 data points)
Time elapsed: 00:00:19.630963
msbenchmark spectra binary c:\test\B06-11071.mzML
Enumerating spectra: 6687/6687 (78477534 data points)
Time elapsed: 00:00:14.470447
msbenchmark spectra binary c:\test\B06-11071.mzML
Enumerating spectra: 6687/6687 (78477534 data points)
Time elapsed: 00:00:14.546455
Actually I'm not sure why mzML is faster here - even though mzXML to mzML means copying the binary
data twice instead of just once, I would expect that to be offset by the bloated metadata in mzML.
These were both converted from RAW with the same settings: no peak picking, default precision (which
in mzML is 64-bit for m/z, 32-bit for intensity, but in mzXML it's 64-bit for both).
It's a good idea to explain your benchmarking practice when you come out with
"factor ~7" ;)
-Matt
On 8/30/2012 4:16 AM, Thomas Dybdal Pedersen wrote:
Hi
I've recently begun to investigate whether it was time to change our pipeline
from mxXML to mxML
format. Our pipeline is partly based on xcmd which uses RAMP to read in ms
data. I quick comparison
of the parsing speed between mzML and mzXML showed that mzML was slower by a
factor ~7. This is
quite substantial especially for larger files.
I understand that the mzML parsing is based on pwiz instead of implemented from
the ground, which is
probably the cause for the difference. Is there any effort in creating a more
effecient parser for
the mzML format as this format increase in relevance?
with best wishes
Thomas
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/spctools-discuss?hl=en.
