Background and Methods: Using a nanoparticle-based enrichment (Proteonano) methodology on human plasma samples, we achieved a substantial increase in identified proteins from ~700 to >5000 proteins compared to neat plasma digest. In a small-scale pilot test, we applied this methodology to a small cohort of plasma samples from pancreatic cancer (PC) patients with different disease stages: (I) primary tumor and (II) metastases, and compared them with healthy controls. Most identified proteins are within the Human Plasma Proteome Project (HPPP) database, and more than 300 proteins are on the list of FDA-approved drug targets.Results: We observed a large and significant increase in ribosomal proteins in the plasma of patients with metastatic PC. ADH1C and ADH1B, both members of the alcohol dehydrogenase family, were particularly upregulated in patients with liver metastasis. Fifteen other predicted secreted and/or cell surface–associated proteins with known cancer associations are also significantly altered and would otherwise go undetected in neat, digested plasma.Conclusions: The significant increase in proteome depth allows a strong foundation for future large-scale experimental and comparative analysis. Lastly, similar conclusions could be reached from comparing different mass spectrometers (Orbitrap Astral and Orbitrap Ascend) and columns (depth and throughput) setups on the same dataset, although the depth approach on the newer Orbitrap Astral instrumentations can reveal additional insights in the plasma proteome.
背景与方法：通过对人血浆样本采用基于纳米颗粒的富集技术（Proteonano），与未经富集的血浆酶解样本相比，我们鉴定出的蛋白质数量从约700种显著提升至超过5000种。在一项小规模初步试验中，我们将此方法应用于一组来自不同疾病分期胰腺癌患者的血浆样本：（I）原发性肿瘤期与（II）转移期，并与健康对照组进行比较。大部分鉴定出的蛋白质均收录于人类血浆蛋白质组计划数据库，其中300余种蛋白质属于美国食品药品监督管理局批准的药物靶点。 结果：我们观察到转移性胰腺癌患者血浆中核糖体蛋白呈现显著且大幅度的增加。酒精脱氢酶家族成员ADH1C与ADH1B在肝转移患者中表达上调尤为明显。另有15种已知与癌症相关的预测分泌蛋白和/或细胞表面相关蛋白也发生显著变化，而这些蛋白在未经富集的血浆酶解样本中无法被检测到。 结论：蛋白质组覆盖深度的显著提升为未来开展大规模实验与比较分析奠定了坚实基础。最后，通过对同一数据集采用不同质谱仪（Orbitrap Astral与Orbitrap Ascend）及色谱柱（深度模式与高通量模式）配置进行比较，我们得出了相似结论，但采用新型Orbitrap Astral仪器的深度分析模式能够进一步揭示血浆蛋白质组中更多潜在信息。
肿瘤(癌症)患者之家