The differentiation of inks on a questioned document can highlight a fraudulent insertion and is usually carried out by optical comparison and Thin-Layer Chromatography (TLC). Laser Desorption Ionization Mass Spectrometry (LDI-MS) may also be used for the analysis of dyes from ink. This analytical technique was compared to a standard method of High Performance Thin Layer Chromatography (HPTLC) according to their capacity to differentiate blue ballpoint inks. Ink entries on paper from 31 blue ballpoint pens have been analyzed and their dye ink formulations compared. The pens were classified into 26 classes by LDI-MS against 18 for HPTLC. LDI-MS proved to be a more powerful method for differentiating ink formulations because it provides information about dye structures (molecular weights) and relative quantification of dye classes (peak areas). Sample preparation was minimal and analysis time was short in contrast to the more complex extraction, application and development steps of the HPTLC method. However, only basic dyes and pigments were identified using positive mode LDI-MS, while HPTLC did yield additional information about acid dyes.