mProphet discrepancy between Skyline Versions

support
mProphet discrepancy between Skyline Versions doellingerj  2018-02-16 05:34
 
Dear Skyline Team,

thanks for the amazing Software!!!

I am currently working on DIA data generated on a QE instrument. When I analyze one run using Skyline Version 3.5.0.9321 I can detect 13058 Peptide Sequences with q < 0.01 using mProphet. When I open the same document, which was generated in Version 3.5.0.9321, in Skyline 4.1.0.11714 and reintregrate the data using mProphet I can only detect 10662 Peptides with q < 0.01. What is the reason for this large difference and how can I get back my "lost" peptides?

kind regards

Joe
 
 
Brendan MacLean responded:  2018-02-16 15:02
Hi Joe,
I would like to have a look at your document. Can you post it to the following drop point? (Use File > Share - Complete to create a .sky.zip file.)

http://skyline.ms/files.url

There have been changes for sure between 3.5 (1-Dec-2015) and 4.1 (11-Jan-2018). Hopefully all improvements, which would mean the statistics were less accurate in estimating 1% FDR at 13058 peptides, but maybe there was some kind of regression in your case.

The change is extreme enough that I would be very interested in having a look. If you will share your file, I will see what I can find.

Thanks for reporting it.

--Brendan
 
doellingerj responded:  2018-02-26 00:02
Hi Brendan,

unfortunately I "do not have privileges to this directory. Verify that you are signed in appropriately."

Do I need another account for uploading?

kind regards

Joe
 
Nick Shulman responded:  2018-02-26 05:07
Joe,

All users on this website are supposed to have permissions to upload on that page.
Can you attach a screenshot of what your browser looks like when you are seeing the "not have privileges" message?

You are supposed to end up on this page:
https://skyline.ms/project/home/support/file%20sharing/begin.view?
but it sounds like you might have ended up somewhere else.
 
doellingerj responded:  2018-02-26 06:12
Hi,

I have attached the screenshot.

kind regards

Joe
 
Nick Shulman responded:  2018-02-26 14:16
Hi, Joe,

It looks like you did upload a file with the name "Skyline Version discrepancy.sky.zip" on Feb 18, 2018.
You do have permission to upload new files, but you do not have permissions to delete or replace files.

If you want to upload another file, then you will have to give it a new name.
Is the file that you uploaded last week the one that you want Brendan to take a look at?
 
doellingerj responded:  2018-02-27 00:43
Hi Nick,

yes, "Skyline Version discrepancy.sky.zip" uploaded on Feb 18, 2018 is the correct file.

best regards

Joe