[Psidev-qc-dev] HUPO-PSI Quality Control Working Group

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

Hi, Sue and Robert.

I am writing in connection with my work in the HUPO-PSI Quality Control Working Group.  We were founded in April as a way to facilitate the use of quality control workflows with proteomics and metabolomics data sets.  Several groups have now produced tools to generate proteomics quality metrics from raw data or raw data plus identifications.  Our working group hopes to put forward standard ways to communicate these metrics (particularly a file in an updated "qcML" format), making it possible to make downstream decision-support tools that are able to work with a variety of front-end metric generators.

We believe one of the important ways we can leverage these metrics is by ensuring that data sets that reach publication have some basic quality information accompanying them (for some tools, this would mean spending just a few minutes of CPU time to generate the qcML document).  The qcML document could, for example, inform potential users of the numbers of MS/MS scans acquired, the proportion of precursors that were +2, or the distribution of TIC throughout the MS scans.

We submitted a manuscript to Analytical Chemistry that introduced the goals of the working group to solicit input from the broader community.  A reviewer has suggested that we need to show greater clarity on how we will interact with journals to nudge publication guidelines to recommend the inclusion of qcML once the format is finalized and the tools to produce them are easily acquired.  The two of you came to my mind as great resources on how this evolution could take place.

Do you have some insights on how receptive ACS and ASBMB journals would be to including this recommendation for proteomics and metabolomics manuscripts?

Thank you,
Dave