Platelet extracellular vesicles (PEVs) are emerging as key biomarkers in diabetes mellitus (DM), reflecting altered platelet function and coagulation pathways. This study compares two proteomic techniques—nanoLC-MALDI-MS/MS and nanoLC-TIMS-MS/MS—for analyzing PEVs in diabetic patients, to assess their potential for biomarker discovery. PEVs were isolated from platelet-rich plasma and characterized using tunable resistive pulse sensing (TRPS), Fourier-transform infrared (FTIR) spectroscopy, and transmission electron microscopy (TEM). Proteomic analyses identified significant differences in protein expression between diabetic and non-diabetic individuals, with nanoLC-TIMS-MS/MS demonstrating superior sensitivity by detecting 97% more unique proteins than nanoLC-MALDI-MS/MS. Key differentially expressed proteins included apolipoproteins and oxidative stress markers, which may contribute to platelet dysfunction and cardiovascular complications in DM. Sex-specific variations in protein expression were also observed, highlighting potential differences in disease progression between male and female patients. The integration of advanced proteomic methodologies provides novel insights into the role of PEVs in diabetes pathophysiology, underscoring their diagnostic and therapeutic potential. These findings pave the way for improved biomarker-based strategies for early detection and monitoring of diabetic complications.