MSStats "invalid labels length" error message

MSStats "invalid labels length" error message juapebe  2018-09-28

Hi all,
I am unable to run MSStats on my dataset. I am able to do it with other similar size datasets, and actually I can still do it with an older version (pre-curation) of this one, but somehow now It wont run. Here's the error message I am getting:
Error in factor(work$RUN, levels = unique(work$RUN), labels = seq(1, length(unique(work$RUN)))) :
invalid 'labels'; length 2 should be 1 or 0
Error : Can't process the data.
Error in runComparison() :
Can't finish analysis.

I also downloaded the file and tried running it on my local R MSstats implementation (on a MAC) and it works! So it is something related to how Skyline is formatting the output for the one installed there.


Nick Shulman responded:  2018-09-28
Can you send us your Skyline document?
In Skyline, you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms. If that .zip file is less than 50MB then you can attach it to this support request. Otherwise, you can upload it here:

-- Nick
juapebe responded:  2018-10-07
Thanks for the offer for help. I was able to figure out the issue, and it comes from MSStats itself rather than the Skyline implementation:
When you have multiple fractions that share some peptides (in my case I did this for a set of internal standard proteins), MSstats does not know how to deal with them. Solving this issue is trivial when using the R native app but it would be nice if skyline could deal with them prior sending them to msstats for analysis as well.