Boxcar support DiegoB  2020-05-13

Hi Skyline team
I was wondering if Skyline support MS1 filtering on data acquired using Boxcar on the Exploris.
Thanks a lot

Brian Pratt responded:  2020-05-13

Hi Diego,

We haven't implemented support for this, but I'd be happy to work with you on it. Do you have any data you can share? Ideally a raw file and a Skyline document (use File>Share>Complete),. You can upload to or we can work something else out. I expect Skyline will show a strange spiky chromatogram extraction at the moment, but we'll get that sorted out.

Thanks for using the Skyline support board!

Brian Pratt

Brendan MacLean responded:  2020-05-17

So far we have only been able to work with the data from the original paper, which we are not sure is the best representation of how the files from the Exploris are formatted.

Can we possibly get any data from you, as Brian has requested?

DiegoB responded:  2020-05-17

Hi Brendan and Brian
Sure we will upload some data today, we had some issue with the mass spec last week.
Thanks for your help.


Brian Pratt responded:  2020-05-19

Thanks. You can drop it at or we can arrange anything (dropbox etc) that's convenient for you.


DiegoB responded:  2020-05-20

I just uploaded a zip called dbt containing a mab digest acquired in DDA and Boxcar with a Skyline file where I entered the most intense peptides unmodified. I will refine the ms1 filtering so that we can compare results between the two acquisition methods.
Thanks a lot

Brian Pratt responded:  2020-05-20

Hi Diego,

The files look good, thanks for the upload. We'll look into understanding the boxcar metadata in the raw file, and how Skyline should use it.


matt.chambers42 responded:  2020-05-21

Hi Diego,

We noticed the Boxcar file doesn't have DDA MS2s like the paper describes. Have you been able to analyze these data in MaxQuant? I'm able to get results from the DDA file but not from the Boxcar file (in a separate param group with Type=Boxcar and "Match between runs" turned on).

DiegoB responded:  2020-05-21

HI Matt in my knoledge the raw schould contain top 5 dda. Will look into it tomorow.

DiegoB responded:  2020-05-22

Hi Matt
I just checked in lab with the team, the Boxcar was acquired on the Exploris 480 running Xcalibur, I attached the settings used where it seems to me that top 5 DDA is enabled in parallel with the Boxcar. I just notice that the size of the Raw is quite small compared with the DDA and I was expecting the opposite.
We do not use MaxQuant and even if we are in drug development install a new soft requires an IT approbation, still this can be done if the soft is not available on your side.

matt.chambers42 responded:  2020-05-22

Hi Diego, I'm not sure what's going on. I do see the DDA function in QualBrowser's instrument method, but there's no MS2 scans in the file. And like you noticed, it's also much smaller than the regular DDA file.

DiegoB responded:  2020-05-22

I will recreate the method and rerun it. Will also drop a mail to thermo.
I will upload a new file by monday.

matt.chambers42 responded:  2020-05-26

Hi Diego,

Did you manage to fix the issue? I forgot to mention before, is it normal that there are 2 experiments in the method that totally overlap in their time start/stop points?

DiegoB responded:  2020-05-29

HI Matt
There are 2 experiments one fore dda and the other for boxcar.
I repeted the aquisition reproducing the problem. I'm waiting for a feedback from Thermo.
Aside the missing dda did you manage to get the boxcar ms1?

I will keep you posted

Jacob responded:  2021-07-15

Hi All,

Currently playing with using skyline for analysing boxcar DIA. I was wondering if there was any progress with the MS1 filtering? Happy to help if i can.


Brian Pratt responded:  2021-07-21

This hasn't come to the top of our development list, sorry.

Best regards,

Brian Pratt

Jacob responded:  2021-07-21

No worries. It sort of works anyway, the MS1 just looks messy.