Decomposition of five amino acids, alanine, serine, cysteine, aspartic acid, and asparagine, under irradiation with soft X rays (magnesium Kalpha X-ray source) in ultra-high vacuum was studied by means of X-ray photoelectron spectrometry (XPS) and mass spectrometry. A comparative analysis of changes in XPS line shapes, stoichiometry and residual gas composition indicates that the molecules decompose by several pathways. Dehydration, decarboxylation, decarbonylation, deamination and desulfurization of pristine molecules accompanied by desorption of H2, H2O, CO2, NH3 and H2S are observed with rates depending on the specific amino acid. NEXAFS spectra of cysteine at the carbon, oxygen and nitrogen K-shell and sulfur L2,3 edges complement the XPS and mass spectrometry data and show that the exposure of the sample to an intense soft X-ray synchrotron beam results in the formation of C-C and C-N double and triple bonds. Qualitatively, the amino acids studied can be arranged in the following ascending order of radiation stability: serine<alanine<aspartic acid<cysteine<asparagine.