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

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

Hi, Karl.

I am part of a working group at HUPO-PSI that seeks to further the use of quality control pipelines in conjunction with proteomics and metabolomics experiments.  We are pretty familiar with tool sets for dealing with general identification data, but we would like to give some concrete examples of experiments that are less well-covered by quality control tools.  iTRAQ and TMT came to mind, and I recalled some conversations we had back in the CPTAC Data Analysis teleconferences that touched on this subject.

Have you gone ahead to create tools for producing quality control metrics in iTRAQ or TMT experiments?  For example, one might ask what fraction of MS/MS scans include reporter ions from all four channels (if one uses the 4-way reagent, of course).  I believe you were on your way to computing such metrics.

I hope to include some concrete examples of how quality control becomes more concrete in specialized areas of proteomics and metabolomics as part of a manuscript we are fielding to Analytical Chemistry that introduces our working group and its goals to a broader audience.

Thanks!
Dave