Detecting proteins via surface assisted laser desorption/ionization mass spectrometry (SALDI-MS) method is still highly challenging, and only few examples of nanomaterials have been demonstrated to perform such detection so far. In this study, carbon nanowalls (CNWs), vertically aligned graphene sheet-based materials, presenting specific morphology, dimensions, and boron doping levels have shown improved performances for both qualitative and quantitative detection of Cytochrome C under optimized experimental conditions. Boron doped carbon nanowalls (B-CNWs) with a [B]/[C] ratio of 5000 ppm and growing time of 4 h have shown the best performance in terms of signal intensity and reliability. Then, the detection of ricin, a ribosomal-inhibiting protein (RIP) classified as category B bioterrorism agent by CDC (Centre of Disease and Control and Prevention), was performed. For the first time, direct SALDI-MS detection of ricin B chain was reported without tedious sample preparation steps or database interrogation, and results were obtained within few minutes and a limit of detection (LOD) of 0.5 pmol/μl was obtained. Thanks to the introduction of galactosamine residues on B–CNW, we were able to selectively detect ricin B chain protein in complex media such as serum and soft drinks with enhanced signal intensity. B-CNWs are not toxic and are adaptable to any commercial MALDI-TOF mass spectrometer, showing their great potential as SALDI based materials.