Can skyline import the raw data on a remote hard disk?

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Can skyline import the raw data on a remote hard disk? andyzcq  2013-07-27
 
I am a newbie for Skyline.
Recently I acquired SWATH data on TripleTOF 5600, and want to use Skyline to analyse SWATH data.
I imported raw data on a hard disk on LAN,but there are always some errors happening.
When I analyse the raw data on local disk, everything is working fine.

So I want to ask whether Skyline can handle the data on a remote hard disk.
 
 
Brendan MacLean responded:  2013-07-28
Yes. Usually, Skyline can import data directly from a remote drive. Most of my data is on a network disk, and I know several close collaborators who work this way also.

What is the error you are seeing?

--Brendan
 
andyzcq responded:  2013-07-28
Thanks for your reply.
I simultaneously imported 10 SWATH files into skyline.
When I analyzed a target peptide using skyline, 9 of 10 files showed traces of product ions but one of them do not, which is indicated in the attached figure.
It is wield that when I analyze another peptide, 10 files all show traces of product ions.
I do not know what is going wrong.
 
Brendan MacLean responded:  2013-07-29
That would seem to indicate that the run in question did not actually contain any MS/MS scans with isolation windows containing your precursor of interest.

That is at least the first thing to double-check. Maybe something went wrong with the SWATH method and no MS/MS scans were collected for the range of that precursor for that run.

If you are totally sure that this is not the case, then we can arrange for you to send me both the Skyline document and the WIFF file that is behaving strangely and I can take a closer look.

Thanks for using Skyline for your DIA data analysis.

--Brendan
 
andyzcq responded:  2013-07-30
wiff file is very big (about 1.5G).
You mentioned that something went wrong with SWATH method, and I checked my SWATH method.
The attached figure is the SWATH method in my skyline software.
In data acquiring computer, the precursor ion isolation windows in the analyst are different, which also in the attachment.
Actually I do not know how to set the same SWATH method in the skyline as in the analyst.
 
Brendan MacLean responded:  2013-07-30
I don't know that this will solve your problem, but from the Analyst image you sent, your method in Skyline should be:

400.5 - 424.5 - 0.5
424.5 - 449.5 - 0.5
449.5 - 474.5 - 0.5
474.5 - 499.5 - 0.5
etc.

So, your current method is incorrect. We will try to make the interface for entering these methods in Skyline more intuitive.

But, I don't think this is explains the problem you are seeing with your data.

I will send you instructions on how to send me your Skyline document and the 1.5G WIFF file that is having the problem.

Thanks for your time in investigating this issue.

--Brendan
 
andyzcq responded:  2013-07-31
The skyline document and wiff file are being uploaded to FTP.
I have a stupid question.
Why is the setting of 400.5-424.5-0.5 in the skyline equal to 400-425 in the analyst?
 
Brendan MacLean responded:  2013-07-31
Okay, I will have a look.

You may be interested in this issue I posted in response to your confusion:

https://skyline.gs.washington.edu/labkey/issues/home/issues/details.view?issueId=257

In working on the isolation scheme editor, we eventually concluded that there were two different "windows" involved in setting up an isolation scheme:

1. The instrument isolation window, or the range you actually set the instrument to isolate
2. The extraction window, or the range from which you want Skyline to extract ion chromatograms

My initial design for the feature was to use #1 as the only think shown to the user, since I expected people like you to be using the feature, arriving with an existing instrument method.

However, in working on the feature, it became clear that this was also confusing to people, and it was actually clearer to people that they had contiguous non-overlapping extraction ranges, when that was expressed in the ranges displayed in the grid. So, we decided to switch to displaying #2.

Now I am willing to try figuring out a way to offer to display either way. Hopefully that will make it clearer.

We also had in mind some kind of graphical display, but never quite got to that.

Thanks for posting your data. Hope that helps to clarify a little.

--Brendan