This project investigates the fundamental limits of efficient algorithms for solving combinatorial problems through formal mathematical reasoning frameworks known as proof systems. These systems form the theoretical basis of widely used algorithmic methods such as SAT solvers, algebraic techniques, integer programming, and semidefinite programming hierarchies. Despite their practical success, a theoretical understanding of why these algorithms perform well, or fail, on real-world instances remains larely incomplete. The main objectives are to establish strong impossibility results, specifically average-case lower bounds and supercritical trade-offs, on the size or depth of proofs in three key proof systems: Resolution, Cutting Planes, and Sum-of-Squares. The mathematical methods developed have broader implications, including advances in pseudo-random matrix analysis and circuit complexity. Practically, these results clarify the inherent hardness of fundamental computational and learning problems beyond worst-case scenarios, offering guidance for future algorithm design by ruling out futile heuristics.