[Psidev-qc-dev] HUPO-PSI communication of quality parameters

[Tabb, D. P. [<dt...@su...>]

Hi, Meena.  I hope that you enjoyed a good holiday weekend!


I am writing in connection with my work on mzQC, a file format for communicating quality information about biological mass spec data.  Our working group for mzQC formed after the 2016 HUPO-PSI Workshop at Ghent.  Our goal is to design a format for passing qc data from metric generation tools (like QuaMeter IDFree) to metric analysis tools (like outlier detectors) and metric storage databases.  Wouldn't it be nice to be able to perform outlier detection from many different metric generators?  At first, we intended to use an XML-based format, like qcML, but we have shifted to a lightweight JSON format instead.


When we publish mzQC, we want to have a well-established "ecosystem" of tools that can speak the mzQC format.  Your MSstats toolkit already has a solid track record, so we would love to work with you to enable mzQC output.  We're just about done with the file specification, so the course to that implementation would probably look like this:


1) Together we select a particular analysis workflow to adapt for this purpose (MSstats can handle lots of different types of experiments, so we might select a most common route to model in the first case).

2) We add terms to our controlled vocabulary that relate to the different metrics that your software outputs.

3) Your team adds the JSON output capability, and we ensure our mzQC readers can validate the JSON your code outputs.


Would something like this be feasible in the next twelve months or so?


I know that's it's always hard to find the time for features like this, but we hope that our work on streamlining the format requirements will make this a relatively easy task.


Thanks,
Dave

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