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• The ESI FT-ICR MS was applied for studying kraft lignin modification by T. hirsuta. • The main patterns of lignin modification were determined. • The groups of systematically degraded and released compounds were identified. • The main enzymes used by the fungus were versatile and manganese peroxidases. • The order of peroxidase secretion was connected with lignin modification patterns. The process of kraft lignin modification by the white-rot fungus Trametes hirsuta was investigated using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS), and groups of systematically changing compounds were delineated. In the course of cultivation, fungus tended to degrade progressively more reduced compounds and produced more oxidized ones. However, this process was not gradual – the substantial discontinuity was observed between 6th and 10th days of cultivation. Simultaneously, the secretion of ligninolytic peroxidases by the fungus was changing in a cascade manner – new isoenzymes were added to the mixture of the already secreted ones, and once new isoenzyme appeared both its relative quantity and number of isoforms increased as cultivation proceeded. It was proposed, that the later secreted peroxidases (MnP7 and MnP1) possess higher substrate affinity for some phenolic compounds and act in more specialized manner than the early secreted ones (MnP5 and VP2). [ABSTRACT FROM AUTHOR]