Targeted Assays with Waters Synapt

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Targeted Assays with Waters Synapt msielaff  2019-08-01
 

Hi everybody,
Following problem: We acquired targeted runs on a Waters Synapt G2-S. Five MS2 channels were recorded, one for each precursor. When importing these raw files (screenshot of full-scan settings is attached), Skyline only extracts fragment ion information from the second channel, which is also the case when the MS/MS filtering method is set to DIA. The other four channels are ignored.
Is there a way/workaround to import the other channels in Skyline, too?

Thanks!
Malte

Skyline version 19.1.0.193
Windows 7

 
 
Brian Pratt responded:  2019-08-01
Hi Malte,

If you can provide the Skyline document (use File > Share > Complete to create a .sky.zip file) and the raw Waters data, I am sure we can figure this out quickly. You can upload those to http://skyline.ms/files.url .

Best Regards,

Brian Pratt
 
msielaff responded:  2019-08-01
Dear Brian,

I uploaded the zipped skyline project and two test files of the mentioned format.
2019-029_skyline_project.sky.zip
O190713_10.raw.zip
O190713_14.raw.zip

Thank you very much for the fast response and your help!

Best regards
Malte
 
Brian Pratt responded:  2019-08-01
I think the only problem is that you indicated to Skyline that the data needs lockmass correction, in which case Skyline assumes that channel 3 is special. For the transition list you have, and the selection ions in the data (401.25 1023.5 754.93 461.2 652.91) it seems to be working properly when you don't ask for lockmass correction.

Best Regards,

Brian Pratt
 
msielaff responded:  2019-08-02
Hm, very interesting! How do the data look like when you import the raw files? Are the different channels displayed in the same chromatogram? I tried to import the raw data again and it still imports only the second channel (see attached screenshots). I also left the lockmass field empty when importing the data. Would it be possible to provide your Skyline document with all the imported channels?
 
msielaff responded:  2019-08-02
To exclude issues with other software / hardware configurations (see attached screenshot, system_information_1), I installed Skyline on another computer (system_information_2) and replicated the analysis. Unfortunately, Skyline still extracts information only from channel 2.

Best regards
Malte
 
Brian Pratt responded:  2019-08-02
Hi Malte,

Consider the selected ions in the raw data:
401.25
461.2
652.91
754.93
1023.5

And the precursor m/z values in your document:
460.776211
652.350271
754.866688
801.421342
1023.448344
1295.596799

and your Transition Settings > Instrument > Method Match Tolerance:
0.055

and you can see that only the 1023.448344 precursor can be expected to match the raw data:
460.776211    -    461.2    =    -0.423789
652.350271    -    652.91    =    -0.559729
754.866688    -    754.93    =    -0.063312
1023.448344    -    1023.5    =    -0.051656

Try increasing that match tolerance and you'll get more chromatograms.

Best,

Brian Pratt
 
msielaff responded:  2019-08-02
It works!!! It's the first time I work with targeted data and I never really considered the Method Match Tolerance parameter. Your support here is amazing! Thank you very much, Brian!
 
Brian Pratt responded:  2019-08-02
Ausgezeichnet!