Re: [Psidev-ms-dev] Spectra with length 0 in mzData files

[Randy J. <rkj...@in...>]

This question is a good one to address again as we consider various 
changes to the schema.  The essential goal is to allow schema-level 
validation where the content of the <data> element is required in the 
schema definition.  Thus, the element cannot be left empty, but what 
should we do when the mass spectrometer reports (and records) a totally 
empty spectrum?  Currently we are suggesting this be handled as given 
below - report a 0 length data array and put 0 in for mass and 
intensity.  Several instrument vendor do it this way (and report this 
information using their API's).  This seems preferable over not 
recording the spectrum, or putting length="1" and then having an invalid 
mass value of 0.  This most often occurs when the export from the vendor 
format file is performed with a threshold which sets a minimum intensity 
value on what is exported - a spectrum full of noise might be reported 
as 'empty'.  Even when no user threshold is set, I have seen 'empty' 
spectra recorded in the raw binary data for an instrument even through 
electronically this makes almost no sense.

Does anyone have any other suggestions which improve the reporting of an 
empty (but recorded) spectrum?

Your other question is language dependent.  If you map to Java, 
precision="32" is a float, and precision="64" is a double.  Other 
languages have other precisions for internal representations, but the 
idea is the "32" is an IEEE 4 byte float and "64" is an IEEE 8 byte float.

Has anyone else had any problems using the precision attribute?

Randy

> I'm writing a viewer for mzData files and have come across a small
> problem where I'm not sure if it's me or the data files which are wrong.
>
> I'm decoding the Base64 data in the spectra and am using the myo_ms2.xml
> file from sourceforge as an example.  However my parser is falling over
> on the following lines:
>
> <mzArrayBinary>
>                 <data precision="32" endian="little" 
> length="0">AAAAAA==</data>
> </mzArrayBinary>
> <intenArrayBinary>
>                 <data precision="32" endian="little" 
> length="0">AAAAAA==</data>
> </intenArrayBinary>
>
> In these cases the file specifies a length of 0, despite there being 1
> value in the entry (albeit 0 and 0).  Is this the correct way of
> denoting an empty spectrum, or should this file really quote a length of
> 1?
>
> Also whilst I'm asking - can anyone point me to a reference for the
> correct way to handle 64 bit precision data on a 32bit machine and vice
> versa?  I'm kind of new to a lot of this low level binary stuff!
>
> Cheers
>
> Simon.
>
> -- 
> Simon Andrews PhD
> Bioinformatics Dept
> The Babraham Institute
>
> sim...@bb...
> +44 (0)1223 496463
>
>
>
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