Issue 569: Trouble in importing Altis SRM data in skyline daily

issues
Status:resolved
Assigned To:matt.chambers42@gmail.com
Type:Defect
Area:Skyline
Priority:1
Milestone:4.1
Opened:2018-04-02 by Gao
Changed:2018-10-16 by Brendan MacLean
Resolved:2018-10-16 by Brendan MacLean
Resolution:Fixed
Closed:
2018-04-02 Gao
Title»Trouble in importing Altis SRM data in skyline daily
Assigned ToGuest»Brendan MacLean
Type»Defect
Area»Skyline
Priority»1
Milestone»4.1
I am having trouble importing data generated on Altis into skyline daily. The data was scheduled 2800 transitions using 90 min LC gradient so the size of the data is about 200M. It takes over 10 min to import the data and sometimes the skyline file will randomly close by itself in the middle of the importing. Attached please see the screenshot while the data is importing.

I am just wondering whether there is anything I can do to make the importing goes faster. Thank you so much!

2018-04-06 matt.chambers42
I didn't have any problems with random crashing while converting the file outside Skyline, but I did find way to improve performance. I have tested with Thermo's newer file reading API and the SRM chromatogram access has a lot of potential for speedup. With the current one-transition-at-a-time enumeration, the new API is possibly faster than the old one, but not by much (and I haven't compared the actual chromatogram data points to make sure they're the same). But the new API also supports requesting multiple chromatograms at a time; when I request all 2800 transitions at once, it finishes in a mere 15 seconds. It also uses about 800MB of RAM.

Notwithstanding the extra RAM usage, it's probably worth it to switch to this all-transitions-at-once enumeration after ProteoWizard has switched to using the new Thermo API.

2018-10-16 Brendan MacLean
resolve as Fixed
Statusopen»resolved
Assigned ToBrendan MacLean»matt.chambers42@gmail.com
64-bit Skyline has been changed to use the new RawFileReader DLL from Thermo. Please try the latest Skyline-daily to see if the problem still persists after this change.