[Psidev-pi-dev] Issue 42 in psi-pi: Issues with the CV

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Comment #39 on issue 42 by dcreasy: Issues with the CV
http://code.google.com/p/psi-pi/issues/detail?id=42

Interesting points Matt, and useful to have feedback from your mzML  
experience.
When the input to the search is an mzML file, our spectrumID attribute is  
the mzML
spectrum 'id'. This is 'easy' and a majority of people agreed at an earlier  
meeting
that if you want further information like retention time, you need to go  
back to the
mzML file.

When the input to the search engine is an mgf file, things are not so easy,  
because
different people use the title, scans and rtinseconds fields in different  
ways. Also,
as you say, there is no guarantee that any of these are unique. In a case  
where
someone has provided say the rtinseconds, but not a title, it would be  
useful to
report this and to make it clear which of the possible values is being  
reported.

Using a zero based index into the MGF isn't an option for the general  
purpose program
that takes a Mascot (.dat) results file and converts it to an analysisXML  
file
because it doesn't have the mgf file and doesn't know what the offset is.

btw, in case it's not clear, we don't currently have a nativeID attribute  
for the
<SpectrumIdentificationResult>

A common use case might be that someone has an anlysisXML document  
originating from
an mgf search and thinks a result looks 'interesting'. They then want to go  
back to
the original 'raw' data to look at it. Ideally, this should take as few  
steps as
possible. The only safe spectrumID value for the Mascot converter is the  
Mascot query
number (this is not what the examples use at the moment). So, the user  
needs the
Mascot (.dat) results file to then find the title/scan/rtinseconds and from  
that can
determine the scan number in the raw data. Seems like a long way round to  
me and
requires that they also have the .dat file.

We are trying to not use userParams too much in analysisXML because we are  
keen to
make the most of the cv validation tools.

So, I realise it's far from ideal, but I think what I'm proposing makes the  
best of a
far from ideal situation. Or maybe I'm missing something?

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