Ultrahigh performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS) was used to analyze a colorant and silk, which were prepared and dyed using shellfish (Hexaplex trunculus L.) purple. Solutions of colorant and silk extracts were analyzed immediately after preparation (fresh samples) and after storing them in the dark for thirty days (aged sample I). Moreover, a silk sample was subjected to artificially accelerated ageing under UV radiation (aged sample II). The application of the UHPLC-MS/MS method leads to the detection of (i) the major coloring components of shellfish purple, which are indigotin, indirubin, 6-bromoindigotin, 6′-bromoindirubin, 6-bromoindirubin, 6,6′-dibromoindigotin, 6,6′-dibromoindirubin; (ii) four minor indigoid components in shellfish purple (compounds A, B, C and D), which belong to the same structural class as indirubin, and whose identification has been reported only once in the past; and (iii) eight degradation products (isatin, degradation products DP3, DP4, DP5, DP6, DP7, DP9 and DP10). The latter were also detected in stored indigotin solution, except for DP 6, which was used as reference sample. The method development was assisted by a new solution preparation approach for investigating compound fragmentation, using a solvent system compatible with direct infusion ESI. This system replaceddimethyl sulfoxide, which inhibits detection through electrospray ionization.