Dear Skyline team,

We are presently attempting to assess the benefits of using multiplexing to assist in the label free quantification of complex samples, trialing this on a HeLa protein standard. The tutorial on how to do this was clear and simple to follow and we have acquired our MSX scans. However, the import of these result files into Skyline is incredibly slow. While we expected it to be slow given the tutorial said upfront that one user reported a 20 hour import time for a 200 MB file several years ago, a single result file is importing at a rate of ~2% per day (our files are just shy of 200 MB each). Because we expected it to be slow, we used slightly less windows than in the tutorial for our trial (4 windows of width 6m/z). Data is from a Q-Exactive HF-X and our library size is quite large as we are doing untargeted proteomics, so roughly 55,000 peptides and 680,000 transitions. We are currently running version 4.2.0.19009 of Skyline on a Windows 10 machine with 64GB RAM and a 6 core hyper-threaded Xeon processor. I thought our computer was of reasonable specs so was wondering if you had a sense of why the import is slow; are we simply not meant to be doing untargeted proteomics with MSX or is it likely we have messed up a setting? Please let me know if you need any files or more information.

Many thanks,

Tim