A prostate cancer tissue specific spectral library for targeted proteomic analysis

Proteomics. 2022 Apr;22(7):e2100147. doi: 10.1002/pmic.202100147. Epub 2021 Dec 1.

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: SWATH-MS spectral library; high-pH fractionation; prostate cancer; targeted proteomics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Formaldehyde / chemistry
  • Humans
  • Male
  • Mass Spectrometry
  • Paraffin Embedding
  • Prostatic Neoplasms*
  • Proteins
  • Proteomics* / methods
  • Tissue Fixation

Substances

  • Proteins
  • Formaldehyde