Fraction handling DIANNtoMSstatsFormat

[CCLab]

Dear MSstats Team,
I have question regarding fractionated samples and the DIANNtoMSstatsFormat converter. I fractionated a whole proteome sample into two fractions for three biological replicates, measured them by DIA and analysed the results with DIANN.

In the DIANNtoMSstatsFormat function I want to set "summaryforMultipleRows = sum" since I have fractions and not technical replicates, but it is just ignored. Is there a way to change this?

Thanks for developing this awesome package.

Best,

Tim

[Anthony Wu]

Hey Tim,

So there's a few things I want to highlight:

• For fractionated experiments, if a fragment ion is measured in multiple fractions, then MSstats will pick the fraction with the most measurements across all samples.  If there is a tie (e.g. in your case, if a fragment ion is measured in both fractions across all three biological replicates), then MSstats will pick the fraction with the greatest sum intensity (which seems to be your intention).
• summaryForMultipleRows is only applied for cases when there are duplicate PSMs in a single MS run.  So this parameter doesn't modify the fraction selection behavior described in the first bullet point above.

Thanks,

Tony