Targeted Mass Spectrometry of a Clinically Relevant PSA Variant from Post-DRE Urines for Quantitation and Genotype Determination

Proteomics Clin Appl. 2020 Nov;14(6):e2000012. doi: 10.1002/prca.202000012. Epub 2020 Jul 9.


Purpose: The rs17632542 single nucleotide polymorphism (SNP) results in lower serum prostate specific antigen (PSA) levels which may further mitigate against its clinical utility as a prostate cancer biomarker. Post-digital rectal exam (post-DRE) urine is a minimally invasive fluid that is currently utilized in prostate cancer diagnosis. To detect and quantitate the variant protein in urine.

Experimental design: Fifty-three post-DRE urines from rs17632542 genotyped individuals processed and analyzed by liquid chromatography/mass spectrometry (LC-MS) in a double-blinded randomized study. The ability to distinguish between homozygous wild-type, heterozygous, or homozygous variant is examined before unblinding.

Results: Stable-isotope labeled peptides are used in the detection and quantitation of three peptides of interest in each sample using parallel reaction monitoring (PRM). Using these data, groupings are predicted using hierarchical clustering in R. Accuracy of the predictions show 100% concordance across the 53 samples, including individuals homozygous and heterozygous for the SNP.

Conclusions and clinical relevance: The study demonstrates that MS based peptide variant quantitation in urine could be useful in determining patient genotype expression. This assay provides a tool to evaluate the utility of PSA variant (rs17632542) in parallel with current and forthcoming urine biomarker panels.

Keywords: genotype; mass spectrometry; parallel reaction monitoring; post-digital rectal exam urine; prostate cancer.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Biomarkers, Tumor / genetics
  • Biomarkers, Tumor / urine
  • Chromatography, Liquid / methods
  • Digital Rectal Examination / methods
  • Genotype
  • Humans
  • Kallikreins / genetics
  • Kallikreins / urine*
  • Male
  • Mass Spectrometry / methods
  • Polymorphism, Single Nucleotide
  • Prostate-Specific Antigen / genetics
  • Prostate-Specific Antigen / urine*
  • Prostatic Neoplasms / genetics
  • Prostatic Neoplasms / pathology
  • Prostatic Neoplasms / urine*


  • Biomarkers, Tumor
  • KLK3 protein, human
  • Kallikreins
  • Prostate-Specific Antigen