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A prostate cancer tissue specific spectral library for targeted proteomic analysis |
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| Authors: | Rui Sun Mengge Lyu Shuang Liang Weigang Ge Yingrui Wang Xuan Ding Cheng Zhang Yan Zhou Shanjun Chen Lirong Chen Tiannan Guo |
| Institution: | 1. Zhejiang University, Hangzhou, Zhejiang, China
Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China;2. Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China;3. Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou, China;4. Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China;5. Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China |
| Abstract: | Prostate cancer is the most common cancer in males worldwide. Mass spectrometry-based targeted proteomics has demonstrated great potential in quantifying proteins from formalin-fixed paraffin-embedded (FFPE) and (fresh) frozen biopsy tissues. Here we provide a comprehensive tissue-specific spectral library for targeted proteomic analysis of prostate tissue samples. Benign and malignant FFPE prostate tissue samples were processed into peptide samples by pressure cycling technology (PCT)-assisted sample preparation, and fractionated with high-pH reversed phase liquid chromatography (RPLC). Based on data-dependent acquisition (DDA) MS analysis using a TripleTOF 6600, we built a library containing 108,533 precursors, 84,198 peptides and 9384 unique proteins (1% FDR). The applicability of the library was demonstrated in prostate specimens. |
| Keywords: | high-pH fractionation prostate cancer SWATH-MS spectral library targeted proteomics |