MSstats DIA error

MSstats
MSstats DIA error trinidad martin  2016-10-03
 
Hello all!!

First of all thank you very much for this amazing software!!

I am currently running:

Skyline (64 bits) 3.5.0.9319
R version 3.2.4 (2016-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
MSstats_3.3.11

The problem is while running the QC for my DIA samples within Skyline.

I have 6 samples, 3 biological replicates and 2 different conditions:
mock1
rap1
mock2
rap2
mock3
rap3

And I have this error:
"*** Subject : 1, Condition : Mock has multiple rows (duplicate rows) for some ENDOGENOUS features ()"
"*** Subject : 1, Condition : Rap has multiple rows (duplicate rows) for some ENDOGENOUS features ()"
"*** Subject : 2, Condition : Mock has multiple rows (duplicate rows) for some ENDOGENOUS features ()"
"*** Subject : 2, Condition : Rap has multiple rows (duplicate rows) for some ENDOGENOUS features ()"
"*** Subject : 3, Condition : Mock has multiple rows (duplicate rows) for some ENDOGENOUS features ()"
"*** Subject : 3, Condition : Rap has multiple rows (duplicate rows) for some ENDOGENOUS features ()"
"ERROR : Please remove duplicate rows in the list above. "

My question is how can I know the duplicated field?? what do you mean with ENDOGENOUS features??
And, I guess I cannot remove my duplicates within skyline, can I??

Thank you very much!!!!

T
 
 
Nick Shulman responded:  2016-11-04
I am sorry that no one answered this question. MSstats questions are supposed to be asked in the MSstats Google Group:
https://groups.google.com/forum/#!forum/msstats

I can tell you that "Endogenenous" means "light IsotopeLabelType" and "Feature" means "Transition".
There was another person who had a similar question about MSstats choking on duplicate rows:
https://skyline.gs.washington.edu/labkey/announcements/home/support/thread.view?entityId=7941c864-847b-1034-b804-da202582a216

If the answer I gave to the other support request is not helpful, then you should ask your question in the MSstats Google Group, because that group is monitored by people who are better experts than I am.
 
trinidad martincampos responded:  2016-11-04
Thanks a lot for the information!! I will have a look ;)