Thermobifida fusca, a thermophilic bacterium belonging to Actinobacteria, is a major degrader of plant cell walls. The protein profiles of the secretome produced by T. fusca grown in cellulose, lignin, and mixture of cellulose and lignin containing culture media, promoting production of respective substrate hydrolyzing enzymes, was explored using a proteomics approach with high throughput isobaric tag for relative and absolute quantification (iTRAQ) technique using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The iTRAQ quantification of the secretome revealed unique extracellular enzyme system, including discrete multienzyme complexes of cellulases, hemicellulases, glycoside hydrolases, proteases, peroxidases, and protein translocating transporter proteins. When the strain was grown in these substrate conditions, proteins corresponding to cellulases, hemicellulases and transport proteins were highly up-regulated, while lignin degrading DyP-type peroxidase, novel nonheme peroxidases, catalase, cytochrome-c oxidase, and superoxide dismutase were also identified. Numerous proteins presumed to be involved in lignocellulose hydrolysis were expressed in response to these different culture conditions, and among these were several secreted hypothetical proteins that were not previously observed.