Unlock the secrets of melanoma progression with our latest deep dive into proteomic analysis, where cutting-edge size-exclusion chromatography meets DIA-MS to reveal the intricate protein profiles of extracellular vesicles in plasma and serum.
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Size-exclusion chromatography combined with DIA-MS enables deep proteome profiling of extracellular vesicles from melanoma plasma and serum.
Lattmann et al., Cell Mol Life Sci 2024
<!– DOI: 10.1007/s00018-024-05137-y //–>
https://doi.org/10.1007/s00018-024-05137-y
Streamlined Workflow for Profiling Melanoma EV Proteins
A new experimental workflow has been developed to profile proteins from extracellular vesicles (EVs) in the blood of healthy donors and melanoma patients. This method, called SEC-DIA-MS, integrates size-exclusion chromatography with data-independent acquisition mass spectrometry, allowing for deep proteomic profiling with minimal sample input. Remarkably, using just 200 µL of plasma, the study identified 2,896 EV-associated proteins, which is a 3.5-fold increase in depth compared to previous melanoma research.
Additionally, the researchers employed an automated protocol to deplete the most abundant proteins from plasma and serum, which roughly doubled the protein group identifications compared to unenriched blood. The EV proteome was distinct from unenriched plasma and serum and could differentiate between samples from healthy donors and melanoma patients. Notably, melanoma markers like MCAM, TNC, and TGFBI were upregulated in melanoma EVs but not in depleted plasma, underscoring the unique and specific information EVs carry.
The study also found that EVs were significantly enriched in intact membrane proteins and proteins linked to SNARE interactions and T-cell biology. This advancement in EV-based proteomic analysis is significant as it can be applied to larger patient cohorts and potentially extended to other diseases, enhancing its utility as a tool for biomarker discovery.