Discovery or shotgun proteomics has emerged as the most powerful technique to comprehensively map out a proteome. Reconstruction of protein identities from the raw mass spectrometric data constitutes a cornerstone of any shotgun proteomics workflow. The inherent uncertainty of mass spectrometric data and the complexity of a proteome render protein inference and the statistical validation of protein identifications a non-trivial task, still being a subject of ongoing research. This review aims to survey the different conceptual approaches to the different tasks of inferring and statistically validating protein identifications and to discuss their implications on the scope of proteome exploration.