Proton Elastic Scattering Analysis (PESA) is a simple convenient method for hydrogen analysis in thin samples. A Proton Induced X-ray Emission (PIXE) target chamber was equipped with a PIPS detector for detection of forward-scattered protons. One of the objectives was to perform PIXE and PESA analyses of air particulate targets simultaneously. Tests and calibrations were fulfilled mainly with Mylar foils 1.5–6.5 μm thick in the proton energy region between 1.35 and 2.3 MeV. The energy dependence of scattering cross section is different from the Rutherford formula. Comparison of PIXE/PESA analysis with the Guelph Scanning Proton Microprobe Laboratory at the University of Guelph, Canada on seven aerosol samples was carried out. The intercomparison results validated our PESA/PIXE quality assurance protocol. In addition, repeated measurements of Gelman TefloTM filters indicated a gradual increase of hydrogen content by 1 ng/cm2 per 1 μC/cm2 proton dose.