Performing XPS on Pt–Ru/C nanoparticles
However, my problem is that I'm not getting clear enough peaks. The obvious thing I can think of to do is increase the number of scans or lengthen the dwell time.
But I was wondering if there are other solutions other people usually
do that I might be missing. I do see some papers that try to
deconvolute Ru and C in the same region but my professor says that
this is an incorrect method because it is impossible to consider the
correct charge correction that way.

Do you have an Atlas of XPS spectrum of elements? Check the instrument's manual. I do recall CASA used to have element by element spectrum.
Thermo Fisher has one periodic XPS spectrum here. If gold is causing problems, choose another metal whose peaks do not overlap with your sample.
The only solution for weak signals is that you collect the data for a longer time (ensemble averaging).
Don't try deconvolution in XPS especially when it is peak fitting. Your mentor is right. It is not reliable. You can fit as many peaks as you like. There must be a rationale for fitting peaks in an analytical signal (you exactly know peak shapes, peak model, baseline etc.)