MaxQuant version 2.8.0.0 possible new "Reverse" column name

[Ian VanGordon]

Hi,

I was using a MaxQuant output for the first time with MSstats. I ran MaxQtoMSstatsFormat then dataProcess and realized there were "REV_" (reverse) sequences in the processed_data$ProteinLevelData slot. Looking back at an old MaxQuant output shows that the decoy columns used to be named "Reverse" in the proteinGroup.txt and evidence.txt output files. Using MaxQuant 2.8.0.0 the "Reverse" column is now missing from these files and there is a new column called "Decoy" that seems to represent the same information. Although I couldn't find any documentation of this change, I believe this is why I saw reverse sequences in my processed data. 

I reran MSstats but changed "Decoy" column names to "Reverse" in the proteinGroup and evidence data which resulted in MSstats removing decoy sequences and they were no longer present in the processed data. 

I just thought I would see if you all agree with this conclusion to make sure I am not doing something wrong and if so, to let you all know for future versions of MSstats.

Thank you for an awesome package!

Ian

[Anthony Wu]

Hey Ian,

Thank you for letting us know about this change in MaxQuant; I don't think we would've known about this change without your input.  I agree with your conclusion and we'll make an update in the next release of MSstats to account for this change as a result.

Tony