The purpose of this study was to optimize quantitative electron energy loss spectroscopy (EELS) of elements that have characteristic edges in the low energy loss region and are components of organic matrices. The optimum parameters for phosphorus L 2,3-edge (at 135 eV) detection were determined by numerical analysis of computer-generated, Poisson-noisy spectra and by experimental measurements (at 80 keV) of films of the phosphoprotein, phosvitin. When the first, second and third valence electron/plasmon scatterings are included in the multiple least-squares (MLS) fit, the background subtraction of (first-difference) spectra is significantly more accurate than that obtained with the “inverse power law” method, even for a specimen thickness of only 0.25λ. Taking into account the effects of plural scattering, the optimal thickness for P quantitation is approximately 0.3λ. Signal-to-noise ( S / N) ratio decreases rapidly with thickness, and at 1.0λ, it is only about 60% of the optimum S / N. The combined effects of the statistical uncertainty of measurements and of the systematic error due to gain variations of the parallel detector were evaluated, and the relative sensitivities of the no-difference (raw spectrum), first-difference and second-difference methods were compared. For channel-to-channel gain variations greater than 0.1% and up to 0.8%, the first-difference method results in the lowest uncertainty of P measurements. In the absence of gain variations, direct fitting provides the greatest sensitivity (least uncertainty), whereas at larger gain variations it may be necessary to use the second-difference method. The optimum energy shift for collecting a first-difference spectrum, approximately 15 eV, did not show any great variation between 5 and 25 eV, and is, in general, specimen dependent. Quantitation with EELS showed excellent correlation with simultaneous electron probe X-ray microanalysis, but, for the detection of P in a 0.25λ thick specimen, EELS was approximately five to six times more sensitive than X-ray. The minimal detectable P concentration, with 0.5 nA beam current for 100 s in a 0.25λ thick specimen, was 8.4 mmol/kg (0.01 at%) at the 99% confidence level, equivalent to 34 phosphorus atoms for a 15 nm probe. This value is close to the theoretical prediction of 7.5 mmol/kg, and can be improved only by further reducing the gain variation and directly fitting the non-difference spectrum. Appropriate reduction of the gain variations to less than 0.1% would result in a further, approximately two-fold, improvement in the parallel EELS detection system. However, in order to obtain the optimal specimen thickness for phosphorus quantitation in cryosections, it will be necessary to use higher (approximately 200 keV) excitation voltages.