Re: [Psidev-ms-dev] additional feature request: precursor m/z method logging?

[Matthew C. <mat...@va...>]

Hi Josh,

I'm not sure I like the idea of this rather subtle difference being all 
the way up at the software/processing level. Instead, what if, for 
Thermo accurate mass instruments, the filter line m/z and the 
monoisotopic trailer m/z had their own CV terms, so a precursor block 
might look like:

<precursorList count="1">
              <precursor spectrumRef="S19">
                <ionSelection>
                  <cvParam cvLabel="MS" accession="MS:1000040" 
name="m/z" value="445.34"/>
                  <cvParam cvLabel="MS" accession="MS:1000041" 
name="charge state" value="2"/>
                  <cvParam cvLabel="MS" accession="MS:1000xxx" 
name="Xcalibur scan filter line m/z" value="445.51"/>
                  <cvParam cvLabel="MS" accession="MS:1000xxx" 
name="Xcalibur monoisotopic trailer m/z" value="445.34"/>
                </ionSelection>
                <activation>
                  <cvParam cvLabel="MS" accession="MS:1000133" 
name="collision-induced dissociation" value=""/>
                  <cvParam cvLabel="MS" accession="MS:1000045" 
name="collision energy" value="35" unitAccession="MS:1000137" 
unitName="electron volt"/>
                </activation>
              </precursor>
</precursorList>

In this case, it is clear which method was used for picking the primary 
m/z value. In the case of someone writing their own precursor m/z 
picking routine, that new software would have both a generic CV term 
referencing the software in the software/processing block, and also its 
own precursor m/z CV term, like:
<cvParam cvLabel="MS" accession="MS:1000xxx" name="msPrefix m/z" 
value="445.338"/> (in addition to this value being used as the primary 
m/z value)

But it also seems to be that any or all of this information is 
relatively useless from a machine's perspective. Quantitative 
information about how accurate the m/z value is would be more helpful on 
that front, e.g.:
<cvParam cvLabel="MS" accession="MS:1000xxx" name="m/z accuracy" 
value="2" unitAccession="MS:1000xxx" unitName="ppm"/>

-Matt


Eric Deutsch wrote:
> From: Joshua Tasman 
>
> Hi all,
>
> Can we figure out a way to add a note regarding the determination of the
> precursor m/z ("parent" m/z)?  There are a few ways to do it for Thermo
> software with the Xcalibur API, at least, and I can imagine that someone
> might write their own processing routines to include in the converters.
>
> So: 1) can we clarify that the software/processing section can handle
> multiple entries for the same software (for example, "thermo API filter
> line", "thermo API trailer label value", etc.
> and 2) some way to reference this near the info at the scan level?
>
> Thanks,
>
> Josh
>
>
>