Question about filtering conditions with MSstats quantification

[mstaniak]

Hi,

when I see the message:

WARNING! the number of unique conditions in evidence file are different from the conditions in contrast!
                                  All the extra conditions will be deleted from the evidence file

what happens exactly and how is data processed for MSstats quantification?

Kind regards,
Mateusz

[biodavidjm]

Hi @mstaniak ,

you might have included a number of conditions samples when searching the data with MaxQuant, but if some of them are not included in the contrast.txt file (or in the "keys.txt" file), those samples would be ignored before proceeding with the MSstats analysis

David

[mstaniak]

This filtering is done before summarization (dataProcess in MSstats) and model fitting (groupComparison in MSstats), right?