failed to install MSstats from the Tools store

support
failed to install MSstats from the Tools store chenxiaotong  2020-04-01
 

Dear Skyline Team,
At the very beginning, I can successfully install the MSstats tool in my computer, but it couldn't work and an error was reported in the immediate window as shown in the attach file below. And then, I tried to replace the R 3.5.0 with R 3.6.1 which has the "caTools" package that can be installed. But the skyline kept reminding me to install the R, then I installed and uninstalled MSstats and R again and again. And suddenly, I couldn't install the MSstats anymore and an new error was reported in the immediate window as shown in the attach file below.
Best Regards,
Xiaotong Chen

 
 
Nick Shulman responded:  2020-04-01
Xiaotong Chen,

You should install R version 3.5.0 again.

You can have multiple versions of R installed on your computer at the same time. The MSstats external tool requires R version 3.5.0.

The error that you are getting is "File not found". Skyline is attempting to run the R.exe which is included with R version 3.5.0.

You might find a little more information about that error here:
https://skyline.ms/announcements/home/support/thread.view?rowId=37089

-- Nick
 
chenxiaotong responded:  2020-04-01
Nick,

Thank you for your help. I re-installed R version 3.5.0 and the MSstats can be installed again. Skyline and MSstats can generated its output as expected.

My problem has been solved. Thank you very much.

— Xiaotong Chen
 
chenxiaotong responded:  2020-04-02
Nick,

I met a problem about data analysis. When I ran the MSstats, an error was reported as followed:

 =======================================
 ** Reading the data for MSstats.....
** Peptides, that are used in more than one proteins, are removed.
** Truncated peaks are replaced with NA.
** Intensities with great than 0.01 in DetectionQValue are replaced with zero.
** 14750 features have all NAs or zero intensity values and are removed.
** 18067 features have 1 or 2 intensities across runs and are removed.
** 21 proteins, which have only one feature in a protein, are removed among 3459 proteins.
Some DetectionQValue have no value. Please check "Result Grid" in View.

Error in runComparison() :

 Can't finish analysis.

And I checked the " Result Grid"(shown in the attached file), but I don't know what the matter is.

Xiaotong Chen
 
Nick Shulman responded:  2020-04-02
The MSstats external tool insists that either all of your peptides have q-value, or none of them do.

There is some information about this error here:
https://skyline.ms/announcements/home/support/thread.view?rowId=37570

That page talks about the two workarounds available to you:
1. You can use "Refine > Reintegrate" so that Skyline will calculate a q-value for everything (you might have to also check the "Override manual integration" checkbox.
2. You can remove the "Detection Q Value" column from the MSstats external tool report in the Document Grid.
-- Nick