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Topic: Excalibur: Exporting exact mass list.  (Read 1782 times) previous topic - next topic

Excalibur: Exporting exact mass list.

I am trying to export an exact mass list for direct infusion data using the Q-Exactive.
If I go to export: Clipboard: Export: Clipboard (Exact Mass)
the m/z is off even after setting 5ppm and .xxxx decimal places in the Mass Options.
For example I get:
89.059671   3189961.5
89.059471   3031701.75
89.05987           2126474.25
89.059272   1919686.5
... etc.
When these should all be one mass.
So I thought of a few methods:
Maybe convert my data from profile to centroid:
I was having trouble as the centroid option is not showing up for me.
Maybe go to View: Spectrum List
and then
Display Options: All Peaks
But this doesnt give all peaks... for example in a wide m/z range it gave peaks up to about 2000 intensity, and than in a narrower range it gave peaks up to an intensity of 10.
Any help would be greatly appreciated

Re: Excalibur: Exporting exact mass list.

Reply #1
Hi Jeremy,

Try to copy it through the peak list rather than directly from the spectrum. After displaying the peak list, you can copy that (by right-mouse click) in exact mass or nominal mass to the clipboard.
The mass options you mention do not influence the numbers you copy - the numbers you copy are the measured values - those mass options are to display any ions within the given ppm range for a mass range or base peak chromatogram.

Hope this helps.,

Justin

Re: Excalibur: Exporting exact mass list.

Reply #2
The mass differences you listed look like what could be expected over an infusion run; depending on the mass resolution chosen.  You may need to export the list to Excel if you want to sum up the areas of the "different" masses.

The centroid option will only be available for an "advanced" user; just use the drop-down box to change from Standard.

There is probably a limit to how many it will list, although I think it must be very long, as I have had about 100 before now.