Data-dependent ETD MS2

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arledvina
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Data-dependent ETD MS2

Postby arledvina » Tue Nov 15, 2011 11:11 am

Has anyone had any experience setting up a data-dependent method which triggers ETD MS2 scans based upon the presence of diagnostic peaks in a previous MS2 scan using Thermo instrument software? I think this is called a 'data-dependent MS3' experiment type. I would like to try to set this up but I'm doing something quite wrong, as attempts to validate that the method is working using infusion is showing no success.

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Doug
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Postby Doug » Tue Nov 15, 2011 11:30 am

Have done this with successfully with CAD? For instance, MS1-CADMS2-CADMS3. And MS1-ETDMS2-CADMS3. Those should be pretty straightforward right? And if those work and MS1-ETDMS2-ETDMS3 doesn't work I would be concerned that it is not possible without modifying the instrument code.

arledvina
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Postby arledvina » Tue Nov 15, 2011 11:42 am

Hm... not quite what I mean. I would like to perform CAD; if and only if a specific product ion (or ions) is observed, I would also like to perform ETD MS2 on the same precursor.

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Doug
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Postby Doug » Tue Nov 15, 2011 11:46 am

I see. In any case, can you get these experiments to work? MS1-CADMS2-CADMS3. And MS1-ETDMS2-CADMS3.

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Postby arledvina » Tue Nov 15, 2011 12:01 pm

If you mean basing an MS3 off of the results of a previously performed MS2, I can get those to work.

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Postby Craig » Tue Nov 15, 2011 12:33 pm

If I understand you correctly, I think there is an option called "same MS order as referenced scan" or something to that effect in the data-dependent settings which is what you are looking for. Otherwise you just set it up like a standard MS3 experiment.

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Postby arledvina » Tue Nov 15, 2011 1:58 pm

Craig and Doug,

Thanks for the replies... At this point I think the path of least resistance is to just modify the itcl myself. This should be reasonably straightforward. If I ever figure out how to do this through excalibur, I'll post it.

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Postby JasonH » Wed Nov 16, 2011 10:59 am

I don't have ETD on my LTQ-Orbitrap XL, but the setup is as Craig described. You will need to use the "same order as referenced MS scan event". Otherwise it will do data-dependent MS3 on the target ion. I believe you will need to put your product ions m/z values in the "Product Mass List" window. I have used the Neutral Loss List in the past.

There is also a setup difference in Xcalibur depending on whether you do targeted MS3 or data-dependent MS3. In one case you do MS2, MS3, MS2, MS3 while the other you do MS2, MS2, then MS3, MS3. I can't remember which one goes for which experiment type, but if you do the wrong setup the dynamic exclusion list will prevent MS3 triggers in the data-dependent MS3 case. I think in your case it will go MS2, MS3 (with referenced scan event), MS2, MS3 (with referenced scan event).


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