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the prespecified isolation windows are different from that I set in the MS method

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the prespecified isolation windows are different from that I set in the MS method zzhang9  2018-06-01 12:52
 

Hi there,

I tried DIA on Q Exactive HF. The following inclusion list was used for defining the isolation windows:
INCLUSION LIST
15 entries
Mass Formula Species CS Polarity Start End (N)CE MSX ID Comment
[m/z] [M] [z] [min] [min]
377.50000 Positive
423.50000 Positive
459.50000 Positive
493.00000 Positive
526.50000 Positive
560.50000 Positive
595.50000 Positive
633.00000 Positive
673.00000 Positive
718.00000 Positive
772.00000 Positive
839.00000 Positive
933.00000 Positive
1064.00000 Positive
1469.00000 Positive

However, when I import the data into the Skyline, I got the following results:
347.5 407.5 7.00
393.5 453.5
429.5 489.5
463.0 523.0 13.25
496.5 556.5
530.5 590.5
565.5 625.5
603.0 663.0
643.0 703.0
688.0 748.0
742.0 802.0
809.0 869.0
903.0 963.0
1,034.0 1,094.0
1,439.0 1,499.0

It seems something wrong. Do you have any idea about that? Thank you!

Best,

Zhenbin
 
 
Brendan MacLean responded:  2018-06-05 18:21

I think you will find that the difference is purely one of what the numbers in your two lists represent. The first is a set of isolation center m/z values and the second is a list of isolation window m/z ranges (start to end). If you paste your second list into Excel and apply the function =(A1+B1)/2 and fill down for all of the value pairs, you will see that you get the numbers in your first list, as I did.

Hope that helps to clarify. Great validation of the isolation list import method.

--Brendan