Fractionated Data Not Handled With Data Frame Input to proteinSummarization()

[dnusinow]

Hello,

I'm processing data from a fractionated sample and I think I've found a bug in proteinSummarization(). I've built a data frame with all of the necessary columns and proteinSummarization() reads it just fine and returns a result data frame. However when I use a fractionated sample and include the Fraction column protein summaries are returned per fraction/run rather than across all the fractions for the plex.

I dug through the code and as best I can tell the attached patch fixes the issue. I was also able to route around it by directly calling MSconvert::MSstatsBalancedDesign myself using the default for handle_fractions option the way it's done in the various conversion functions shipped with MSstatsTMT. I'm not sure if there's a reason why handle_fractions was set to FALSE for the plain data frame code path through proteinSummarization though. Do you have any guidance on how to handle this? Thank you!

• David Nusinow

protein_summary_fractions_data_frame.patch