REFERENCES
1. Alix-Panabières C, Pantel K. Liquid biopsy: from discovery to clinical implementation. Mol Oncol. 2021;15:1617-21.
2. Li N, Gu Y, Tang J, Li Y, Chen D, Xu Z. Circulating non-coding RNAs and exosomes: liquid biopsies for monitoring preeclampsia. In: Huang T, Yang J, Tian G, Editors. Liquid Biopsies. New York: Springer US; 2023. pp. 263-77.
3. Karaglani M, Panagopoulou M, Cheimonidi C, et al. Liquid biopsy in type 2 diabetes mellitus management: building specific biosignatures via machine learning. J Clin Med. 2022;11:1045.
4. Siravegna G, Marsoni S, Siena S, Bardelli A. Integrating liquid biopsies into the management of cancer. Nat Rev Clin Oncol. 2017;14:531-48.
5. Ignatiadis M, Sledge GW, Jeffrey SS. Liquid biopsy enters the clinic - implementation issues and future challenges. Nat Rev Clin Oncol. 2021;18:297-312.
6. Bronkhorst AJ, Holdenrieder S. A pocket companion to cell-free DNA (cfDNA) preanalytics. Tumour Biol. 2024;46:S297-308.
7. Diaz IM, Nocon A, Held SAE, et al. Pre-analytical evaluation of streck cell-free DNA blood collection tubes for liquid profiling in oncology. Diagnostics. 2023;13:1288.
8. Jordaens S, Zwaenepoel K, Tjalma W, et al. Urine biomarkers in cancer detection: a systematic review of preanalytical parameters and applied methods. Int J Cancer. 2023;152:2186-205.
9. Dorpe S, Tummers P, Denys H, Hendrix A. Towards the clinical implementation of extracellular vesicle-based biomarker assays for cancer. Clin Chem. 2024;70:165-78.
10. Kalluri R, LeBleu VS. The biology, function, and biomedical applications of exosomes. Science. 2020:367.
11. Jeppesen DK, Zhang Q, Franklin JL, Coffey RJ. Extracellular vesicles and nanoparticles: emerging complexities. Trends Cell Biol. 2023;33:667-81.
12. Petroni D, Fabbri C, Babboni S, Menichetti L, Basta G, Del Turco S. Extracellular vesicles and intercellular communication: challenges for in vivo molecular imaging and tracking. Pharmaceutics. 2023;15:1639.
13. Burbano C, Rojas M, Muñoz-Vahos C, et al. Extracellular vesicles are associated with the systemic inflammation of patients with seropositive rheumatoid arthritis. Sci Rep. 2018;8:17917.
14. Johnsen KB, Gudbergsson JM, Andresen TL, Simonsen JB. What is the blood concentration of extracellular vesicles? Biochim Biophys Acta Rev Cancer. 2019;1871:109-16.
15. Nardi Fda S, Michelon TF, Neumann J, et al. High levels of circulating extracellular vesicles with altered expression and function during pregnancy. Immunobiology. 2016;221:753-60.
16. Gershfeld NL, Murayama M. Thermal instability of red blood cell membrane bilayers: temperature dependence of hemolysis. J Membr Biol. 1988;101:67-72.
17. Rous P, Turner JR. The preservation of living red blood cells in vitro: II. The transfusion of kept cells. J Exp Med. 1916;23:239-48.
18. Moore GL. Additive solutions for better blood preservation. Crit Rev Clin Lab Sci. 1987;25:211-29.
19. Gegner HM, Naake T, Dugourd A, et al. Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis. Front Mol Biosci. 2022;9:961448.
20. Geyer PE, Voytik E, Treit PV, et al. Plasma Proteome Profiling to detect and avoid sample-related biases in biomarker studies. EMBO Mol Med. 2019;11:e10427.
21. Alberro A, Iparraguirre L, Fernandes A, Otaegui D. Extracellular vesicles in blood: sources, effects, and applications. Int J Mol Sci. 2021;22:8163.
22. Jamaly S, Ramberg C, Olsen R, et al. Impact of preanalytical conditions on plasma concentration and size distribution of extracellular vesicles using Nanoparticle Tracking Analysis. Sci Rep. 2018;8:17216.
23. Sorber L, Zwaenepoel K, Jacobs J, et al. Specialized blood collection tubes for liquid biopsy: improving the pre-analytical conditions. Mol Diagn Ther. 2020;24:113-24.
24. Berg S, Kutra D, Kroeger T, et al. ilastik: interactive machine learning for (bio)image analysis. Nat Methods. 2019;16:1226-32.
25. Müller T, Kalxdorf M, Longuespée R, Kazdal DN, Stenzinger A, Krijgsveld J. Automated sample preparation with SP3 for low-input clinical proteomics. Mol Syst Biol. 2020;16:e9111.
26. Gillet LC, Navarro P, Tate S, et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics. 2012;11:O111.016717.
27. Gessulat S, Schmidt T, Zolg DP, et al. Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning. Nat Methods. 2019;16:509-18.
28. Consortium. UniProt: the universal protein knowledgebase in 2025. Nucleic Acids Res. 2025;53:D609-D617.
29. Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 2008;26:1367-72.
30. R Core Team. R: a language and environment for statistical computing. MSOR Connect. 2014;1. Available from: https://www.semanticscholar.org/paper/R%3A-A-language-and-environment-for-statistical-Team/659408b243cec55de8d0a3bc51b81173007aa89b [accessed 25 August 2025].
31. Schwanhäusser B, Busse D, Li N, et al. Global quantification of mammalian gene expression control. Nature. 2011;473:337-42.
32. Chitti SV, Gummadi S, Kang T, et al. Vesiclepedia 2024: an extracellular vesicles and extracellular particles repository. Nucleic Acids Res. 2024;52:D1694-8.
33. Mathivanan S, Fahner CJ, Reid GE, Simpson RJ. ExoCarta 2012: database of exosomal proteins, RNA and lipids. Nucleic Acids Res. 2012;40:D1241-4.
34. Aleksander SA, Balhoff J, Carbon S, et al; Gene Ontology Consortium. The gene ontology knowledgebase in 2023. Genetics. 2023:224.
35. Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25-9.
36. Vallejo MC, Sarkar S, Elliott EC, et al. A proteomic meta-analysis refinement of plasma extracellular vesicles. Sci Data. 2023;10:837.
37. Dhondt B, Pinheiro C, Geeurickx E, et al. Benchmarking blood collection tubes and processing intervals for extracellular vesicle performance metrics. J Extracell Vesicles. 2023;12:e12315.
38. Larsson J, Gustafsson P, editors. A case study in fitting area-proportional euler dia-grams with ellipses using eulerr. SetVR@ diagrams. 2018;2018:84-91. Available from: https://ceur-ws.org/Vol-2116/paper7.pdf [accessed 25 August 2025].
39. Krijthe J, van der Maaten L. Rtsne: T-distributed stochastic neighbor embedding using barnes-hut implementation. CRAN 2023. Available from: https://cran.r-project.org/web/packages/Rtsne/Rtsne.pdf [accessed 25 August 2025].
40. Van der Maaten L, Hinton G. Visualizing high-dimensional data using t-SNE. J Mach Learn Res. 2008;9:2579-605 Available from: https://www.jmlr.org/papers/volume9/vandermaaten08a/vandermaaten08a.pdf [accessed 25 August 2025].
41. Van Der Maaten L. Accelerating t-SNE using tree-based algorithms. J Mach Learn Res. 2014:15:3221-45. Available from: http://www.jmlr.org/papers/volume15/vandermaaten14a/vandermaaten14a.pdf [accessed 25 August 2025].
43. Gu Z, Eils R, Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. 2016;32:2847-9.
44. Uhlén M, Fagerberg L, Hallström BM, et al. Proteomics. Tissue-based map of the human proteome. Science. 2015;347:1260419.
45. Atlas HP. The Human Protein Atlas 2024. Available from: https://www.proteinatlas.org [accessed 25 August 2025].
46. Wickham H. ggplot2: elegant graphics for data analysis. Cham: Springer; 2016.
47. Xu S, Chen M, Feng T, Zhan L, Zhou L, Yu G. Use ggbreak to effectively utilize plotting space to deal with large datasets and outliers. Front Genet. 2021;12:774846.
48. Deun J, Mestdagh P, Agostinis P, et al; EV-TRACK Consortium. EV-TRACK: transparent reporting and centralizing knowledge in extracellular vesicle research. Nat Methods. 2017;14:228-32.
49. Livshits MA, Khomyakova E, Evtushenko EG, et al. Isolation of exosomes by differential centrifugation: theoretical analysis of a commonly used protocol. Sci Rep. 2015;5:17319.
50. Théry C, Witwer KW, Aikawa E, et al. Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines. J Extracell Vesicles. 2018;7:1535750.
51. Lucien F, Gustafson D, Lenassi M, et al. MIBlood-EV: minimal information to enhance the quality and reproducibility of blood extracellular vesicle research. J Extracell Vesicles. 2023;12:e12385.
52. Welsh JA, Goberdhan DCI, O'Driscoll L, et al; MISEV Consortium. Minimal information for studies of extracellular vesicles (MISEV2023): from basic to advanced approaches. J Extracell Vesicles. 2024;13:e12404.
53. Németh K, Kestecher BM, Ghosal S, et al. Therapeutic and pharmacological applications of extracellular vesicles and lipoproteins. Br J Pharmacol. 2024;181:4733-49.
54. Szklarczyk D, Kirsch R, Koutrouli M, et al. The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 2023;51:D638-46.
55. Zorova LD, Kovalchuk SI, Popkov VA, et al. Do extracellular vesicles derived from mesenchymal stem cells contain functional mitochondria? Int J Mol Sci. 2022;23:7408.
56. Chetty VK, Ghanam J, Anchan S, et al. Efficient small extracellular vesicles (EV) isolation method and evaluation of EV-associated DNA role in cell-cell communication in cancer. Cancers. 2022;14:2068.
57. Murray MJ, Watson HL, Ward D, et al. “Future-Proofing” blood processing for measurement of circulating mirnas in samples from biobanks and prospective clinical trials. Cancer Epidemiol Biomarkers Prev. 2018;27:208-18.
58. Sato A, Nakashima C, Abe T, et al. Investigation of appropriate pre-analytical procedure for circulating free DNA from liquid biopsy. Oncotarget. 2018;9:31904-14.
59. Chernyshev VS, Rachamadugu R, Tseng YH, et al. Size and shape characterization of hydrated and desiccated exosomes. Anal Bioanal Chem. 2015;407:3285-301.
60. Rikkert LG, Nieuwland R, Terstappen LWMM, Coumans FAW. Quality of extracellular vesicle images by transmission electron microscopy is operator and protocol dependent. J Extracell Vesicles. 2019;8:1555419.
61. Wu JY, Li YJ, Hu XB, Huang S, Xiang DX. Preservation of small extracellular vesicles for functional analysis and therapeutic applications: a comparative evaluation of storage conditions. Drug Deliv. 2021;28:162-70.
62. Nguyen DB, Ly TB, Wesseling MC, et al. Characterization of microvesicles released from human red blood cells. Cell Physiol Biochem. 2016;38:1085-99.