The special issue “plant proteomics 3.0” was conceived in an attempt to address the recent advancements in as well as limitations of current proteomic techniques and their diverse applications to attain new insights into plant molecular responses to various biotic and abiotic stressors and the molecular bases of other processes. proteomics’ focus is also related to translational purposes, including food traceability and allergen detection. in addition, bioinformatic techniques are needed for more confident identification, quantitation, data analysis and networking, especially with non-model or orphan plants, including medicinal and meditational plants as well as forest tree species. this special issue contains 23 articles, including four reviews and 19 original papers.