Redox regulation is a central control element across a broad spectrum of biology. Thioredoxin (Trx), a widely distributed disulfide enzyme, participates in the control of numerous target proteins, thus playing a key role in regulatory processes. Identification of Trx′s targets will therefore aid the elucidation of redox biology. Two recently developed procedures, one based on thiol-specific probes and the other on affinity trapping, have facilitated the labeling or isolation of potential Trx targets that were later identified with proteomic approaches. Accordingly, the number of identified targets in plants has increased to 400. This review describes recent advances in proteomic strategies that are effectively overcoming challenging problems such as the evaluation of target authenticity. Also presented are two industrial research areas, food processing and medical investigation, in which disulfide-related proteomic studies beyond plant biology are underway.