Issue 559: Cannot load msf result file (PD) when building a library

issues
Status:open
Assigned To:matt.chambers42@gmail.com
Type:Todo
Area:Skyline
Priority:3
Milestone: 
Opened:2017-11-28 by pavel
Changed:2019-09-15 by Brendan MacLean
Resolved:
Resolution:
Closed:
2017-11-28 pavel
Title»Cannot load msf result file (PD) when building a library
Assigned ToGuest»Brendan MacLean
Type»Defect
Area»Skyline
Priority»2
Milestone»4.1
Hi,

today my colleague reported an issue with loading msf files when creating the library. Brief description:
- opening the blank document in Skyline
- Go to: Peptide Settings -> Library -> Build
- naming the library (e.g. "test")
- adding the file (e.g. "07192017_03_JK_MD404_alfa_AllTox.msf"), click on "Finish"
- importing process starts parsing, but crashes at the end with the message
"This file does not contain q-values. ..." (detailed error message in the attachment)

Notes:
- tested on several msf files; no difference
- tested on msf file from different locations (hard drive, USB drive, network drive); no difference
- tested in 64bit of Skyline, in versions 3.1.x.x, 3.7.0.11317, 3.7.1.11571 (daily beta); no difference
- tested on 3 computer with Windows 7 (2x 64bit, 1x 32bit): crashed on 2 computers (1x 64bit, 1x 32bit), worked on one 64bit computer. The one working computer does not differ much (Windows 7, 64 bit) from the other 64bit computer that crashed. However, the crashing computers have all Microsoft updates recently updated, whereas the working computer (Skyline v. 3.7.0.11317) has not been updated for about 4 months. I suspect the issue may be related to some update of dotnet framework or other Windows part, but I may be completely wrong.

If you need the msf file, I could it provide privately.

Thank you for your help and work with Skyline!
Best regards,
Pavel

2017-12-19 Brendan MacLean
Assigned ToBrendan MacLean»Kaipo
TypeDefect»Todo
Priority2»3
Milestone4.1»4.2
Maybe we should improve this error message. It seems to generate a lot of support requests, or add a link to it that points to a Tip page that gives a detailed description of the cause of the problem and possible solutions.

Something like this one for missing ID annotations with Mascot searches also most common with older versions of ProteomeDiscover:

https://skyline.ms/wiki/home/software/Skyline/page.view?name=mascot_missing_rt

2019-09-15 Brendan MacLean
Assigned ToKaipo»matt.chambers42@gmail.com
Milestone4.2»
Changing owner to Matt, since he now owns BlibBuild.