A Prostate Cancer Proteomics Database for SWATH-MS Based Protein Quantification

Ammara Muazzam, Davide Chiasserini, Janet Kelsall, Nophar Geifman, Anthony D Whetton, Paul A Townsend

Research output: Contribution to journalArticlepeer-review


Prostate cancer is the most frequent form of cancer in men, accounting for more than one-third of all cases. Current screening techniques, such as PSA testing used in conjunction with routine procedures, lead to unnecessary biopsies and the discovery of low-risk tumours, resulting in overdiagnosis. SWATH-MS is a well-established data-independent (DI) method requiring prior knowledge of targeted peptides to obtain valuable information from SWATH maps. In response to the growing need to identify and characterise protein biomarkers for prostate cancer, this study explored a spectrum source for targeted proteome analysis of blood samples. We created a comprehensive prostate cancer serum spectral library by combining data-dependent acquisition (DDA) MS raw files from 504 patients with low, intermediate, or high-grade prostate cancer and healthy controls, as well as 304 prostate cancer-related protein in silico assays. The spectral library contains 114,684 transitions, which equates to 18,479 peptides translated into 1227 proteins. The robustness and accuracy of the spectral library were assessed to boost confidence in the identification and quantification of prostate cancer-related proteins across an independent cohort, resulting in the identification of 404 proteins. This unique database can facilitate researchers to investigate prostate cancer protein biomarkers in blood samples. In the real-world use of the spectrum library for biomarker detection, using a signature of 17 proteins, a clear distinction between the validation cohort's pre- and post-treatment groups was observed. Data are available via ProteomeXchange with identifier PXD028651.

Original languageEnglish
Article number5580
Issue number21
Publication statusPublished - 8 Nov 2021


  • Blood proteomics
  • Mass spectrometry
  • Peptide
  • Prostate cancer
  • Protein
  • Spectral library

Research Beacons, Institutes and Platforms

  • Lydia Becker Institute
  • Manchester Cancer Research Centre


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