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Front Page › Forums › BioMap › Normalisation
I don’t see very clear how to normalise the data…I’ve tried to substract the intensity of 190 peak of the matrix but it’s not really sucessful. Any idea? How do you normalise your date?thanks.
Substraction will not be successful. Instead, a division by the signal of the internal standard will compensate for matrix effects.
markus
Hi Markus:
I have divided by the intensity of 190 peak as an internal standard…I send you the results…
An example…
An example of normalization with the 190 peak intensity. [file name=Presentation_Biomap_problem.zip size=95809]http://www.maldi-msi.org/images/fbfiles/files/Presentation_Biomap_problem.zip[/file]
Hi LuLu,
Just woundering if m/z 190 is of a full scan data or if it is an extracted ion image (EII).
Because I think one of “value” in the division operation must be a “EII”. That is you can not divide 2 full data set. Hope it helps.
KC
Hi Kchan,
How can I be sure that I have an EII??
Thanks!
O, boy. Okay here is what you do.
[ol]
[li]open your file.[/li][li]Analysis > Plot > Point[/li][li]You will get the spectrum in the plot tool window.[/li][li]zoom into the m/z region you want to substract (190 for you)[/li][li]MIDDLE BUTTON click and drag on the matrix peak. A green bar will appear over your matrix peak.(middle button might be your scroll wheel)[/li][li]An pop up window will appear. You could play around with the Analysis Mode (I use Mean) And for the Output window, pick an empty window. That’s where your mean image (in your case the matrix divisor) will go. [/li][li]You should see a new image appear in the window you speced. On the bottom you should see something like “(mean:189.3432-191.3324)[/li][li]close the spectrum “Plot tool” window[/li][li]Here is the part I get wrong all the time. Highlight the file you open in step 1. This is your numerator. [/li][li]Tools > Calculation > Divide and the divide window will pop up[/li][li]Your Reference is the window with your matrix image. Output to an empty window. [/li][li]Wait.[/li][/ol]
Hope this is what you were looking for. If it works, send beer.
KC
My God…
Thanks KC!
How many beers do you want?