Long import duration of DIA MSE data with iRT

Long import duration of DIA MSE data with iRT david gomez zepeda  2020-02-19

Dear Skyline Team, I'm trying to analyze data acquired in a Synapt HDMS (G1) in MSE (DIA) mode, but file importing is taking around 12 hours for one single file from a single protein (BSA) analyzed in a 1 hour gradient (1.5 GB file), despite using RT prediction from iRT peptides. I'm intending to analyze complex proteomes from 2 hour gradients (8 GB files), so this time for importing would be a problem.
Is there something that I could do to reduce the import time?

Here is the description of the experiment and what I have done:

  1. Injected a BSA in-home digest in nanoLC-MSE using a Synapt G1 with a 1 hour gradient.
  2. Obtained a Prosit Library of the CRAPome (including BSA) and used it for peptide identification
  3. Created a Skyline file including the peptides for BSA only
  4. Imported the RAW data to Skyline without using RTs
  5. Calibrated an iRT model with the iRT prediction in the Prosit Library, using 13 BSA peptides as standards. I'm doing this because I want to use the BSA peptides for iRT calibration in the analysis of complex proteomes.
  6. In a new file I imported the RAW data to Skyline using predicted RTs from the iRT calibration described above, using 5 minute windows. This took about 12 hours.
  7. I have attached the RAW data and the Skyline complete share folder after results import, without further peptide refinement.
  8. PC specifications
    Processor: Intel Xeon CPU E5.2620 v2 @2.10 GHz (2 processors)
    RAM: 64 GB
    OS: Windows 7 64-bit
Brendan MacLean responded:  2020-02-19

What version of Skyline are you using? (Help > About)

There are no attached files, but for files larger than 50 MB, you will need to post them to:


Please ZIP any Waters .raw data folders.

Yes, 12 hours is way beyond anything we have seen ourselves and would be highly interesting to understand and certainly we would want to get it down below 30 minutes for just about any single file.

Thanks for reporting this issue.


david gomez zepeda responded:  2020-02-19

Hi Brendan,

I'm using Skyline (64-bit) (f09d9bed5)

I posted the files in the Sharing Folder:

Thanks for your quick answer and all the work in Skyline.