For mzXML, both arrays have to be the same precision since there is only
a single attribute to specify the precision of the entire base64
element. Pwiz takes the maximum precision of the m/z and intensity
arrays and set that as the precision for mzXML.
-Matt
On 2/23/2010 11:41 AM, bio.x2y wrote:
Hi Matt,
I've had a look at one of the mzXML files generated by msconvert using
default precisions (i.e. I didn't pass any precision flags on the
command line).
The "peaks" element base64 string encodes 128 bits for each peak,
implying that both m/z and intensity values are stored with 64-bit
precision as default, rather than with 64-bit/32-bit as suggested
above. Since the mzXML format seems to insist on a single precision
for both fields (as specified in scan/peaks/@precision), am I
interpreting this correctly?
Thanks,
bio.x2y
On Feb 16, 8:53 pm, Matthew Chambers<[email protected]>
wrote:
Actually those flags are always used if present. They override the
default 64/32 setup for mz/intensity. If you pass --32 or --64, both
arrays will be what you specify. You can use --mz32 and --mz64 to
control the m/z array by itself. The source of the data (Agilent,
Thermo, Waters, mzML, mzXML, etc.) is irrelevant. You can upconvert from
32-bit mzML to 64-bit mzML. This could be useful if some target
consuming application only works with 32 or 64 bit arrays.
-Matt
bio.x2y wrote:
Thanks again Matt.
Following up on your point 2 above, does this mean that the 32/64/mz32/
mz64/inten32/inten64 flags for msconvert are always ignored, or are
they used elsewhere, e.g. for non-Agilent data?
bio.x2y
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