In a hierarchical cosmogony present-day galaxies build up by continuous merging of smaller structures. At a redshift of three the matter content of a typical present-day galaxy is split into about ten individual protogalactic clumps. Numerical simulations show that these protogalactic clumps have a typical distance of about 100 kpc, are embedded in a sheet-like structure and are often aligned along filaments. Artificial QSO spectra were generated from hydrodynamical simulations of such regions of ongoing galaxy formation. The metal and hydrogen absorption features in the artificial spectra closely resemble observed systems over a wide range in HI column density. Detailed predictions of the column density as a function of impact parameter to protogalactic clumps are presented for HI,CII,CIV,SiIV,NV and OVI. The expected correlations between column densities of different species and their role in understanding the physical properties of the gas from which galaxies form are briefly discussed. The model is able to explain both high-ionization multi-component heavy-element absorbers and damped Lyman alpha systems as groups of small protogalactic clumps.