Parent-ion scanning

Parent-ion scanning r bagshaw  2015-07-22
Will Skyline be able to interpret a RAW file from a parent-ion scanning experiment? In the experiment I specifically want to see parents of a product that is 85. Setting a transition consisting of a parent mass of something I expect to see in the sample with a fragment ion of 85 does not produce a chromatogram in skyline. (this is small molecule work)
Can you comment on this?
Brendan MacLean responded:  2015-07-22
Hi Rick,
I think you are right. For SRM acquisition, we don't really have a way of specifying MS1-level transitions. We certainly do for full-scan (TOF, Orbitrap, ion trap) instruments, but not yet for triple quadrupoles.

I am sure it will be possible to add, if we can get an example of what you are trying to achieve and a raw data file with the chromatogram(s) in it.

You are the first to request it. Maybe because we are so new to small molecule work. At the moment, Skyline currently assumes precursor ion selection in non-full-scan methods (SRM) are actually looking for precursor ions that pass through the collision cell at the fragmentation CE, perhaps to measure fragmentation efficiency, as that was the original request that inspired the addition of precursor ions.

If you get us some data and a clear explanation of the case you are trying to achieve, I am sure we can come up with a way of making it possible in Skyline.

Thanks for your feedback!

karin preindl responded:  2021-01-27
Hello Brandan,
I'm trying to do something similar to Rick and was wandering if you already implemented this feature.

I set up a parent ion scan/precursor ion scan on our sciex qtrap. (the instruments scans in the q1 all parents which produce the product 184).
Now my approach was to set up a transition list with all my possible parent masses and import the raw file but it always gets "chromatogram information unavailable". Also i have to admit i'm new to skyline and i may have got not all the settings right.
Thanks in advance,

Brian Pratt responded:  2021-01-27
If you can provide your Skyline document (use File > Share > Complete) and the Sciex data file, I could have a quick look and see what's going on. You can upload to or we can arrange something more private.


Brian Pratt
Brendan MacLean responded:  2021-01-27
Hi Karin,
I think we will need one of your WIFF files and your current Skyline document (using File > Share - all files to create a single file for upload), which you can post for us at:

Let us know when they are posted and one of us will have a look and get back to you.

karin preindl responded:  2021-01-27
Hello Brendan and Brian,
Thank both of you for the quick reply. I uploaded the files (there are 2 folders- the first contains the wiff and the second is just the zipped skyline document- sorry for the double upload)
Brian Pratt responded:  2021-01-28
Hi Karin,

That's an interesting acquisition mode, and one it seems that we don't currently support. I ran the wiff file through SeeMS and through msconvert to try to understand it better (Skyline, msconvert, and SeeMS all use the same underlying code, so that's a good way to get some insight on Skyline behavior).

From this I can see that it's being read as a bunch of MS2 scans with precursor isolation window of 184.2 +/- 0.5, which is incorrect of course, but you can kind of see where it might arrive at that,

What we want it to be doing, as I understand you, is to be treating those as MS1 scans. (In which case your Skyline document is slightly wonky, there isn't any MS2 data to be had, so your fragment transitions won't ever produce chromatograms though the precursors should).

I'll check with Matt Chambers, our msconvert guru, to see if this is an easy thing to accommodate. From what I can see in the mzML representation there are pretty clear hints as to what's going on so I suspect it won't be too difficult to deal with.

Best regards,

Brian Pratt
matt.chambers42 responded:  2021-01-28
ProteoWizard support precursor (parent) ion scans from Thermo RAW, but not from WIFF. Probably because I'd never seen a precursor ion scan from WIFF. But I'll look at your file and see how much work it would be to add support for it (probably not a lot, but priority is another matter).

Brian, the mzML representation for precursor ion scans is:
ms level = 2 (because fragmentation is occurring, and the monitored fragment intensity is what is being detected)
spectrum type = precursor ion spectrum (this tells you that the m/z dimension refers to the Q1 scanning rather than the Q3)
There is no <precursor>, instead there is a <product> element which looks pretty much the same as <precursor> it just has a different name. And refers to something different semantically of course. The monitored Q3 (product) m/z is in <product>/<isolationWindow> just like isolation m/z would be in a regular MSn spectrum.

Given the differences in mzML representation and semantics, supporting these scans in Skyline is a different issue than supporting it in ProteoWizard. I don't think Skyline would support even precursor ion scans from Thermo right now.
matt.chambers42 responded:  2021-01-28
Actually ProteoWizard partially supported precursor ion scans already, but was putting isolation window in as precursor instead of product elements. That was very simple to fix. Brian may want to weigh in on what support will look like in Skyline.
Brian Pratt responded:  2021-01-28
Well, as long as the representation is consistent it shouldn't be problem - even though it seems pretty hinky to me. Do we have examples of this for Thermo as well?
karin preindl responded:  2021-03-01
Hi Brian,
I just wanted to ask if you are then planning to implement support for wiff parent ion scans in skyline?
Brian Pratt responded:  2021-03-01
Hi Karin,

I can't offer a timeline, but it is on my list. I'm taking on a couple of interns this summer, this might be a good project for one of them.