Composition and Proton Flux from the Solar Wind

I am taking a class on the space environment and I have a few questions about the solar wind. A number of sources list the composition as (approximately) 4% He$^{++}$ and 96% H$^{+}$. What exactly does this mean? Does it mean by mass or by number of ions?

Also, when discussing proton flux due to the solar wind at Earth: What exactly is included in the flux numbers quoted (e.g., one source I have says 2e12 m$^{-2}$s$^{-1}$). Is that the flux due to only the H$^{+}$ and excluding the He$^{++}$ and other minor constituents? Or, are they including all the protons from the other ions as well?

• Just to clarify, it's by number density, not strictly number. – honeste_vivere Jan 17 '17 at 15:51