To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000.

为了满足在临床标本中检测和验证蛋白质生物标志物的日益增长的需求，基于质谱（MS）的靶向蛋白质组学技术包括选定的反应监测（SRM），并行反应监测（PRM）和大规模并行数据独立采集（DIA），已经开发。为了获得最佳性能，他们需要目标肽的碎片离子光谱作为先验知识。在本报告中，我们描述了MS管线和光谱资源以支持针对人体组织样品的蛋白质组学研究。为了构建频谱资源，我们集成了通用的开源MS计算工具，以组装基于Docker的可自由访问的计算工作流。然后，我们将工作流应用于从1696种癌症样品的1096个数据依赖的采集（DDA）MS原始文件中生成了一个完整的DIA泛人类库DPHL。然后将这种广泛的光谱资源应用于17种前列腺癌的蛋白质组学研究（PCa）患者。此后，将PRM验证应用于57位PCa患者的较大研究，并验证了三种蛋白在前列腺肿瘤中的差异表达。作为第二项应用，将DPHL光谱资源应用于一项研究，该研究由19名弥漫性大B细胞淋巴瘤（DLBCL）患者和18名健康对照受试者的血浆样本组成。通过DIA-MS检测DLBCL患者与健康对照组之间差异表达的蛋白质，并通过PRM进行确认。这些数据表明，DPHL支持DIA和PRM MS管线，可用于可靠的蛋白质生物标记物发现。可通过https://www.iprox.org/page/project.html?id=IPX0001400000免费访问DPHL。