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.

Additional Metadata
Keywords Data-independent acquisition, Diffuse large B cell lymphoma, Parallel reaction monitoring, Prostate cancer, Spectral library
Persistent URL dx.doi.org/10.1016/j.gpb.2019.11.008, hdl.handle.net/1765/130310
Journal Genomics, Proteomics and Bioinformatics
Citation
Zhu, T. (Tiansheng), Zhu, Y. (Yi), Xuan, Y. (Yue), Gao, H. (Huanhuan), Cai, X. (Xue), Piersma, S.R. (Sander R.), … Guo, T. (Tiannan). (2020). DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery. Genomics, Proteomics and Bioinformatics. doi:10.1016/j.gpb.2019.11.008