Julianus Pfeuffer
Julianus Pfeuffer
See also #27
I think the defaults are relatively sane right now but we probably should revisit after some more testing. For example, I am not sure about activation_method/fragment_method. MSGF and Comet support...
Hi! That is a good question. Your approach actually could work. But you should probably declare the different voltages as different fractions. 1 1 s1v1.mzML 1 1 2 s1v2.mzML 1...
Hello, Do you really want to compare across FAIMS voltages? If not, try to make the conditions 001,008,010. And in your case, Bio replicate should always be 1. (Unless the...
Great! Actually, I assumed that already. > If **not**, try to .. So, have a look. You should have already intensities per sample.
Hmm yes, this does not look correct. Can you show your current experimental design?
Can you try with consecutive numbers starting from 1 in each column? That means fractions 1,2,1,2,.. And Conditions 1,1,2,2,..
I disagree. Now it seems like you have the correct annotation of conditions. What were you expecting? Do you run the MSstats step? If so, have a look in the...
Regarding your "duplication problem": Duplicated proteins are not the problem. This will be common. The only thing that needs to be resolved are peptides with the same sequence, modification and...
I think version parsing probably just moved to each module.