Proteomic and amino acid profiling of SK-MEL-30 melanoma reveals metabolic and structural changes

Melanoma exhibits high metastatic potential and therapy resistance, driven by metabolic flexibility and structural remodeling. In this study, we performed an integrated analysis of the SK-MEL-30 melanoma cell line using function-focused quantitative proteomics and amino acid profiling. Proteins were quantified using a label-free normalized spectral abundance factor (NSAF) approach, while intracellular amino acids were measured by LC-MS/MS. Functional enrichment analyses based on KEGG and Gene Ontology were used to associate protein expression patterns with metabolic pathways. A total of 148 proteins were identified, predominantly representing high-abundance and functionally relevant components of metabolic and structural pathways. Key cytoskeletal proteins, including vimentin and S100A11, were among the most abundant, consistent with a mesenchymal-like and potentially invasive phenotype. Metabolic profiling revealed elevated expression of glycolytic enzymes such as PKM and LDHA, consistent with a glycolytic shift. Increased levels of l-glutamine and l-glutamic acid, together with GOT2 expression, suggest an active glutamine aspartate axis supporting tricarboxylic acid cycle activity and nitrogen metabolism. In addition, elevated levels of stress-response proteins, including HSP90 and SOD2, indicate a proteostatic network adapted to metabolic stress. Although the proteome coverage is lower than that reported in large-scale deep proteomic studies, the NSAF-based workflow was designed to capture the most abundant and functionally relevant proteins, providing a focused overview of the major metabolic and structural characteristics of SK-MEL-30 melanoma cells. Overall, this integrative analysis highlights the coordination between metabolic reprogramming and cytoskeletal organization in SK-MEL-30 cells and suggests that glutamine-dependent metabolic pathways warrant further investigation as potential therapeutic targets in melanoma.