The early years of philosophical logic saw the characterisation of its basic notions in terms of the axiomatic method. Later, with the invention of Hintikka-Kripke's semantics of modal logic and its extension to other areas of philosophical logic, semantical methods became the dominant approach of philosophers, mathematicians, and computer scientists.

These methods, however, do not reflect the structure of the inferential processes that are necessarily connected to a logical representation.

Modern proof theory was born out of dissatisfaction with the axiomatic logical method and is an attempt at a faithful presentation of the processes of logical inference. The work by Sara Negri in this area was mainly in pure proof theory, from 1997 to 2003, in the tradition of Gentzen, Ketonen, Dragalin and Troelstra. In 2003 she found a way of extending what she had achieved until then to the main areas of philosophical logic. At that time, the development of inferential systems for modal logic and related areas was considered by many an impossibility.

A decisive step in this programme was the formulation of systems of basic modal logic as systems of rules of proof within a well-developed methodology for the analysis of the structure of proofs that she calls proof analysis. The seminal paper in the topic appeared in 2005 and has become a widely cited and very influential work and the basis of several doctoral theses, both in Finland and abroad. An exposition of this theory forms the fourth part of her monograph, co-authored with Jan von Plato, Proof Analysis.