Many proteins undergo post-translational modification via well defined mechanisms such as acetylation, phosphorylation and glycosylation and thereby control a spectrum of biochemical processes. A growing body of evidence suggests that the reversible reduction of disulfide bonds also alters the structure and activity of proteins. Thioredoxin, a ubiquitous 12 kDa protein with a catalytically active disulfide active site (Cys-Gly-Pro-Cys), plays a central role in controlling the redox status of disulfide bonds in proteins that regulate a range of processes. Included are photosynthesis, seed germination, transcription, cell division, radical scavenging and detoxification. The ability to identify unknown functions of proteins of all types has been advanced by the emerging field of functional proteomics. In this brief review, we introduce the disulfide proteome as a tool that complements other methods for the comprehensive analysis of proteins. In so doing, the usefulness of applying this method for both in vitro and in vivo analyses is discussed for thioredoxin and other disulfide proteins, especially those occurring in plants.