In this Perspective, mass spectrometry experiments and chemical dynamics simulations are described that have explored the atomistic dynamics of protonated peptide ions, peptide-H+, colliding with organic surfaces. These studies have investigated the energy transfer and fragmentation dynamics for peptide-H+ surface-induced dissociation (SID), peptide-H+ physisorption on the surface, soft landing (SL), and peptide-H+ reaction with the surface, reactive landing (RL). SID provides primary structures of biological ions and information regarding their fragmentation pathways and energetics. Two SID mechanisms are found for peptide-H+ fragmentation. A traditional mechanism in which peptide-H+ is vibrationally excited by its collision with the surface, rebounds off the surface and then dissociates in accord with the statistical, RRKM unimolecular rate theory. The other, shattering, is a nonstatistical mechanism in which peptide-H+ fragments as it collides with the surface, dissociating via many pathways and forming many product ions. Shattering is important for collisions with diamond and perfluorinated self-assembled monolayer (F-SAM) surfaces, increasing in importance with the peptide-H+ collision energy. Chemical dynamics simulations also provide important mechanistic insights on SL and RL of biological ions on surfaces. The simulations indicate that SL occurs via multiple mechanisms consisting of sequences of peptide-H+ physisorption on and penetration in the surface. SL and RL have a broad range of important applications including preparation of protein or peptide microarrays, development of biocompatible substrates and biosensors, and preparation of novel synthetic materials, including nanomaterials. An important RL mechanism is intact deposition of peptide-H+ on the surface.