Dynamic exclusion mass window

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Biomarker
Albumin Member
Posts: 88
Joined: Thu Aug 09, 2012 3:28 am

Dynamic exclusion mass window

Postby Biomarker » Tue Oct 09, 2012 1:10 am

Hi,

With LTQ orbitrap velos pro, one can lower the mass window of dynamic exclusion setting (in ppm). Does anybody know that in Q Exactive where we can adjust this mass window? I couldn't able to find the same. Does this setting will affect the number of protein IDs?

I look forward to hear from all of you soon.

Cheers....
Biomarker

:)

Kelstrup
Angiotensin Member
Angiotensin Member
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Joined: Fri Oct 05, 2012 5:19 am

Postby Kelstrup » Tue Oct 09, 2012 3:34 am

It's not possible to adjust. I've found it to work nicely though.

cheers,

Chris

Biomarker
Albumin Member
Posts: 88
Joined: Thu Aug 09, 2012 3:28 am

Postby Biomarker » Tue Oct 09, 2012 4:10 am

Hi Chris,

Thanks. If you have seen my earlier post (iTRAQ labelled peptide in Instrumentation forum), you will come to know problem. Orbitrap is identifying more proteins than Q Exactive on the same sample (HCD fragmentation). Is there any other parameter that i need to adjust for iTRAQ labelled peptides on Q Exactive.

Biomarker

Derek
Phosphoserine Member
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Postby Derek » Tue Oct 09, 2012 10:36 am

What are your HCD collision energies for the two MS? They are not equivalent between the two.

What we usually do is run a sample with a HCD energy ramp. We do a Top-2 data dependent with 5 Scan events for each precursor with increasing HCD energy (e.g. MS1, MS2 @25, MS2 @30, MS2 @35, MS2 @40, MS2 @25, MS2 @30, MS2 @35, MS2 @40). We then search the data and filter the number of IDs (quantifiable IDs would be preferred) to find an optimal collisional energy.

Biomarker
Albumin Member
Posts: 88
Joined: Thu Aug 09, 2012 3:28 am

Postby Biomarker » Tue Oct 09, 2012 10:59 am

I used stepping up collisional energy setting, for QE it was 35 with 20 percent and with Orbitrap it was 40 with 10 percent. I don't calling percent is true or nt but it means like for example QE will have like 28 and 42. My method was top 10 data dependant. Is this five scan method is with QE or orbi? And hw? Could you please explain i am naive to this things about 5 Scan events for each precursor. Thanks in advance....


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