My current Skyline project includes signal extraction from a large proteomics spectral library in order to do MS1 and MS2 LFQ. The projects complete successfully, even if it takes time to chug through the library.
However, when I wish to export a report (~10-15 columns), the data export takes an extremely long time - sometimes 12 hours for only 50,000 rows. I have applied filters to reduce the number of rows, but there is always a significant stall when the report is 75-90% complete, regardless of the number of rows.
My questions are 1) any tips on why this may be happening? and 2) is the skyline data accessible any other way? For example, can I write some custom SQL to access file where the data is stored?
Skyline Version: 184.108.40.2065
System: Windows 10 x64, i9-10940x, 64 GB RAM