Beyond Protein Abundance: Proteoform Diversity and Phosphoproteome Remodeling in Maize (Zea mays L.) Responding to Drought and Heat Stresses

Drought and heat stresses are among the most important environmental constraints limiting maize (Zea mays L.) productivity worldwide. Over the past two decades, advances in mass spectrometry-based proteomics have generated extensive datasets describing proteins with altered abundance in maize tissues exposed to water deficit and elevated temperatures. These studies have identified numerous stress-responsive proteins involved in photosynthesis, energy metabolism, antioxidant defense, proteostasis, signaling pathways, and cellular homeostasis. In parallel, phosphoproteomic investigations have revealed extensive remodeling of phosphorylation networks that regulate stress perception, signal transduction, and adaptive responses. However, most available studies remain focused on protein-level observations and provide limited insight into the molecular diversity underlying stress adaptation. This review synthesizes current knowledge on the proteomic and phosphoproteomic responding of maize to drought and heat stresses through the emerging perspective of proteoform biology. We discuss how phosphorylation, oxidative modifications, proteolytic processing, alternative splicing, and genetic variation contribute to proteoform generation and expand the functional complexity of the maize stress proteome. Particular emphasis is placed on the integration of quantitative proteomics, phosphoproteomics, and proteogenomics as complementary approaches for characterizing stress-responsive molecular networks. We further evaluate current methodological limitations, including the predominance of bottom-up workflows, the underrepresentation of combined-stress studies and reproductive tissues, and the limited application of proteoform-resolved analytical strategies. We propose that future advances in maize stress biology will require a transition from protein-centered analyses toward proteoform-centered investigations capable of resolving functionally distinct molecular species. The integration of top-down proteomics, phosphoproteomics, proteogenomics, and systems-level approaches is expected to provide a more comprehensive understanding of stress adaptation mechanisms and facilitate the identification of molecular determinants of climate resilience. Such efforts may ultimately support the development of maize cultivars better adapted to increasingly challenging environmental conditions.