Thank you all for the detailed responses.
JonF, you are correct, the yellow spectrum is a sum spectrum from the map. I did try to upload the same spectrum without the simulated lines, and also a log scale version, but it doesn't seem to have selected properly. I will try again with this post. I didn't even think to simulate with Casino, I am so used to seeing several microns of penetration even at limited kV, but then I am thinking of much lighter metals (Al etc.). The INCA simulation was not fed any parameters at all by me, other than what is built in. I am afraid you are crediting me with more sophistication than is justified! There is a feature in INCA that suggests elements when you click on a peak in the spectrum. Selecting an element from the list of suggestions overlays the purple and green lines onto the spectrum. I would think the default settings are assuming a smooth, polished sample and certainly not thin films and layers. i am still finding my way with the technique and the software, with very limited documentation (and limited brains). Between us, we assigned the small peak between the two main Ir M lines as the Si K line. The Ir peak suggested by INCA that coincides with this is one of the smaller ones. It turns out the substrate is coated with an (unspecified) alloy (it is a crystal from a thin film monitor head), so the Si signal looks very similar either side of the edge of the Ir. I will bear in mind that penetration of the beam in Ir is far lower than I assumed, but I also may have overestimated the Ir thickness, less than 100 nm now looks more likely. Interesting point about the shallow L depth and the low overvoltage - noted, thank you.
Probeman, as above, the only simulation I have is the INCA stock one. I am unsure if INCA varies this spectrum to match the microscope settings at the time. I suspect not.
Jrminter, your suggestions regarding DTSA are gratefully received. It looks slightly daunting, but I will give it a go. Previous discussions have highlighted the need for an Oxford engineer to calibrate the system, but this is not going to happen any time soon due to shortage of cash. It would be handy if I could generate what I need to feed back into INCA to stop all the error messages and enable some more peak ID functionality, but I am not sure if DTSA will help me in this. I must pluck up the nerve to hit the calibrate button on INCA and see what it asks for. Your simulations are interesting. Even with very thin layers, the 2 keV Ir peak is a fair bit larger than the 1.5 keV one, whereas my 1.5 keV dominates. Maybe there is some coincident peak contributing. Thanks for the script, I'll try to pick it apart and identify the bits I need to adjust and give it a whirl - my Python knowledge is very thin. Your point about hammer and nails is very true ("Can't you just stick it in the SEM?").
I take from this lots of extra ideas that I an call on when interpreting what we see. I'll be less inclined to make assumptions about beam penetration, and will make more use of the simulation tools (I'd forgotten that Casino gives the M and L depths). If we get any more results that are relevant to the discussion I'll post them here.
Thank you again for your responses, they are much appreciated. I really don't mind admitting that the extent to which I know what I'm talking about is limited. It's great that you are willing to engage anyway.
We depend on your feedback and ideas!