Supplementary Notes In our paper we present an interpretation of the diffuse very high energy (VHE) -ray emission of the Galactic Centre (GC) region in terms of the interactions of cosmic rays in giant molecular clouds in the region. Here we provide additional discussion of the uncertainties related to the measurement of the -ray flux and spectral index and to the calculation of the energy density and spectrum of cosmic rays in the Galactic Centre region. 1. The total gas mass of the Galactic Centre region The argument that the cosmic ray (CR) flux in the GC region is enhanced over the local density rests on an estimate of the total mass of target material (for CR interactions) in the GC region. The bulk of the gas in the GC region is likely to be molecular hydrogen (H2), which is very difficult to detect directly. Therefore indirect methods of estimating the mass using tracer molecules (or dust particles) must be applied. Tracer molecules are typically rare relative to molecular hydrogen but much easier to detect and with an approximately known ratio to H2. The three mass estimates quoted in our paper are derived via different measurement channels: sub-millimetre emission from dust [16] and line emission from transitions of the CS [14] and C18O [17] molecules. These independent estimates result in CR enhancement factors of 3-9 (CS), 5-13 (C18O) and 46 (dust). Therefore, despite the considerable uncertainties in the mass estimate we find that the hypothesis of a CR density equal to that in the solar neighbourhood (i.e. an enhancement factor of 1) is excluded at a high level of confidence. 2. Uncertainties in the inferred cosmic ray spectrum a) The relationship of the -decay -ray spectrum to the primary hadron spectrum Hadronic interactions of cosmic rays in the interstellar medium lead to the production of neutral pions. The energy spectrum of the -rays produced in the decay of these pions is directly linked to the energy spectrum of the primary cosmic rays. Several authors have calculated the spectral index of the resulting -ray spectrum assuming a power-law for the primary cosmic rays. In the approximation used here [3], the -ray spectral index is identical to that of the primary spectrum. There have been suggestions that the -ray spectrum may be somewhat harder than the primary spectrum, due to scale-breaking effects and the slight energy dependence of the interaction cross-section [S1]. The hardening seen in Figure 6 of [S1] amounts to a difference of 0.04 between the proton and -ray spectral indices. Our own Pythia [S2] simulations confirm that the expected ray spectrum is flatter than the input proton spectrum by about 0.05 in the energy range from 100 GeV to 10 TeV. This difference is a factor of 10 smaller than the observed difference between local and GC CRs observed by H.E.S.S.. Figure 11 of [S3] compares the parameterisation we use ([3], labelled Aharonian Approx.) with that of [S1]. The two curves are in extremely good agreement in the relevant energy range. b) Measurement errors on the -ray spectral index The uncertainty on the -ray spectrum measured by H.E.S.S. includes a statistical and a systematic part. The systematic errors we quote reflect all the non-statistical errors on the spectrum that we are aware of. As the measurement of -rays by a system of Cherenkov telescopes is rather indirect, it is worthwhile to consider the steps involved in the calculation of the -ray energy spectrum and what systematic errors may arise. 1. Production of an electromagnetic cascade by an incident -ray in the atmosphere Electromagnetic interactions in the GeV-TeV energy range are extremely well understood. To confirm that our numerical simulations describe properly the underlying physics, three independent shower simulation codes were compared within the HESS collaboration and no significant differences were found. 2. Production and propagation of Cherenkov light The production of Cherenkov light is also well understood. The uncertainty here stems from the absorption of light in the atmosphere. Comparing our best estimate atmospheric model with a model only marginally inconsistent with our measurements leads to a shift in flux of ~10% but a change in spectral index of only 0.05. These considerations are discussed in detail in [S4] and [S5]. 3. Measurement of a signal in a Cherenkov camera The absolute calibration of the H.E.S.S. cameras has been performed using muon ring images. As the yield of Cherenkov light of a single muon passing through the telescope dish is well known, this signal can be used to calibrate the conversion of Cherenkov photons to electrical signals. Variations of ~10% in the optical efficiency were measured for the data taken on the GC, producing an uncertainty in the absolute energy scale but having little effect on the shape of the reconstructed spectrum. Two independent calibration chains are applied in the analysis of all H.E.S.S. sources and give essentially identical results. 4. Spectral analysis and background subtraction One way a change in spectral slope could arise is due to background subtraction problems. Comparison of different background subtraction models shows differences of <1%, leading to a systematic effect on the spectral index of less than 0.05. Completely independent analyses of the GC (using different shower reconstruction [S6] and spectral reconstruction [S7] techniques) show index variations of < 0.1. Our overall quoted systematic error of 0.2 on the spectral index is a very conservative estimate based on all 4 sources of uncertainty. Considering the field of VHE -ray astronomy as a whole, we note the very good agreement on the Crab Nebula spectrum between the CAT, HEGRA, Whipple, MAGIC and H.E.S.S. instruments as a strong indication that spectra can be well measured at VHE energies. We also note that measurements of the cosmic-ray proton spectrum by the HEGRA instrument at TeV energies [S8] showed good agreement with direct measurements made using satellites and balloons. This overlap with direct measurements provides an additional cross-check of the ground-based air-Cherenkov technique. These notes are the result of discussions with two anonymous referees, whose assistance we acknowledge here. S1. Kamae, T, Abe T. & Koi, T. Diffractive interaction and scaling violation in pp interaction and GeV excess in galactic diffuse -ray spectrum of EGRET. Astrophys. J. 620, 244-256 (2005). S2. Sjöstrand. T, et al. High-energy-physics event generation with Pythia 6.1. Computer Physics Communications, 135, 238-259 (2001). S3. Domingo-Santamaría, E. & Torres, D.F. High energy gamma-ray emission from the starburst nucleus of NGC 253. Astron. & Astrophys. (in press) astro-ph/0506240 (2005). S4. Funk, S. et al. The Trigger System of the H.E.S.S. Telescope Array. Astropart. Phys. 22, 285-296 (2004). S5. Bernlöhr, K. Impact of atmospheric parameters on the atmospheric Cherenkov technique. Astropart. Phys. 12, 255-268 (2000). S6. Lemoine-Goumard, M & de Naurois, M. Advanced analysis methods in the H.E.S.S. experiment. In AIP Conf. Proc. 745: High energy gamma-ray astronomy, 703-708 (2005). S7. Piron, F., et al. Temporal and spectral gamma-ray properties of Mkn 421 above 250 GeV from CAT observations between 1996 and 2000. Astron. & Astrophys. 374, 895-906 (2001). S8. Aharonian, F. et al. The Cosmic Ray Proton Spectrum determined with the Imaging Atmospheric Cherenkov-Technique. Phys. Rev. D. 59, 092003, 1-11 (1999).