The proteins of extracellular vesicles (EVs) that originate from tumors reflect the producer cells’ proteomes and can be detected in biological fluids, e.g., blood plasma. Thus, EVs provide proteomic signatures that are of great interest for cancer diagnostics. By applying targeted mass spectrometry with stable isotope-labeled peptide standards, we assessed the levels of 28 EV-associated proteins, including the conventional exosome markers CD9, CD63, CD81, CD82, and HSPA8, in vesicles derived from the lung cancer cell lines NCI-H23 and A549. Furthermore, we measured their abundance in plasma samples from 34 lung cancer patients and 23 healthy volunteers. Overall, we detected and quantified the levels of seven proteins in undepleted blood plasma: TLN1, TUBA4A, HSPA8, ITGB3, TSG101, and PACSIN2. The most diagnostically potent markers were TLN1 (AUC, 0.95), TUBA4A (AUC, 0.91), and HSPA8 (AUC, 0.88). The obtained EV proteomic signature allowed us to distinguish between the lung adenocarcinoma and squamous cell carcinoma histological types. The proteomic cargo of the extracellular vesicles represents a valuable source of potential biomarkers. This research was funded by the Russian Science Foundation, grant number 21-74-20122. Mass spectrometry analysis and data storage were performed using the equipment of the “Human Proteome” Core Facility (Institute of Biomedical Chemistry).

Cerebrospinal fluid (liquor) samples (N = 44) have been derived from patients with rare tumor hypoglossal schwannoma that comprises about 5% of all non-vestibular schwannomas. Applying high resolution tandem mass-spectrometry 559 proteins were identified with high confidence (at least 2 peptides per protein, FDR <1%) liquor samples. After tryptic digestion, liquor samples were spiked with 148 stable isotopically labelled peptide standards (SIS). Their natural counterparts were mapped onto 111 FDA-approved protein markers. The samples were subjected to alkaline fractionation followed by scheduled multiple reaction monitoring (MRM) of resulted five fractions. The MRM\SIS dataset provides unique quantitative information on proteomic composition of hypoglossal schwannoma liquor samples.

The proteins of extracellular vesicles (EVs) that originate from tumors reflect the producer cells’ proteomes and can be detected in biological fluids, e.g., blood plasma. Thus, EVs provide proteomic signatures that are of great interest for cancer diagnostics. By applying targeted mass spectrometry with stable isotope-labeled peptide standards, we assessed the levels of 28 EV-associated proteins, including the conventional exosome markers CD9, CD63, CD81, CD82, and HSPA8, in vesicles derived from the lung cancer cell lines NCI-H23 and A549. Furthermore, we measured their abundance in plasma samples from 34 lung cancer patients and 23 healthy volunteers. Overall, we detected and quantified the levels of seven proteins in undepleted blood plasma: TLN1, TUBA4A, HSPA8, ITGB3, TSG101, and PACSIN2. The most diagnostically potent markers were TLN1 (AUC, 0.95), TUBA4A (AUC, 0.91), and HSPA8 (AUC, 0.88). The obtained EV proteomic signature allowed us to distinguish between the lung adenocarcinoma and squamous cell carcinoma histological types. The proteomic cargo of the extracellular vesicles represents a valuable source of potential biomarkers. This research was funded by the Russian Science Foundation, grant number 21-74-20122. Mass spectrometry analysis and data storage were performed using the equipment of the “Human Proteome” Core Facility (Institute of Biomedical Chemistry).