title: In silico verification and parallel reaction monitoring prevalidation of potential prostate cancer biomarkers.
abstract: OBJECTIVE
  Targeted proteomics of potential biomarkers is often challenging. Hence, we developed an intermediate workflow to streamline potential urinary biomarkers of prostate cancer (PCa).
  
  
  METHODS
  Using previously discovered potential PCa biomarkers; we selected proteotypic peptides for targeted validation. Preliminary in silico immunohistochemical and single reaction monitoring (SRM) verification was performed. Successful PTPs were then prevalidated using parallel reaction monitoring (PRM) and reconfirmed in 15 publicly available databases.
  
  
  RESULTS
  Stringency-based targetable potential biomarkers were shortlisted following in silico screening. PRM reveals top 12 potential biomarkers including the top ranking seven in silico verification-based biomarkers. Database reconfirmation showed differential expression between PCa and benign/normal prostatic urine samples.
  
  
  CONCLUSIONS
  The pragmatic penultimate screening step, described herein, would immensely improve targeted proteomics validation of potential disease biomarkers.
authors.affiliation: International Centre for Genetic Engineering & Biotechnology, Cape Town, South Africa.|Institute of Infectious Diseases & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa.
authors.forename: Henry A
authors.initials: HA
authors.lastname: Adeola
authors.affiliation: Institute of Infectious Diseases & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa.
authors.forename: Bridget
authors.initials: B
authors.lastname: Calder
authors.affiliation: Institute of Infectious Diseases & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa.
authors.forename: Nelson C
authors.initials: NC
authors.lastname: Soares
authors.affiliation: Urology Department, Grootes Schuur Hospital, Cape Town, South Africa.
authors.forename: Lisa
authors.initials: L
authors.lastname: Kaestner
authors.affiliation: Institute of Infectious Diseases & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa.
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Blackburn
authors.affiliation: International Centre for Genetic Engineering & Biotechnology, Cape Town, South Africa.|Institute of Infectious Diseases & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa.
authors.forename: Luiz F
authors.initials: LF
authors.lastname: Zerbini
mesh_terms: D014408:Biomarkers, Tumor / Q000096:biosynthesis* / Q000652:urine; D003198:Computer Simulation; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D009363:Neoplasm Proteins / Q000096:biosynthesis* / Q000652:urine; D011471:Prostatic Neoplasms / Q000473:pathology / Q000652:urine*; D040901:Proteomics
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins
keywords: biomarkers; in silico; parallel reaction monitoring; prostate cancer; targeted proteomics