title: Proteomics of microparticles with SILAC Quantification (PROMIS-Quan): a novel proteomic method for plasma biomarker quantification.
abstract: Unbiased proteomic analysis of plasma samples holds the promise to reveal clinically invaluable disease biomarkers. However, the tremendous dynamic range of the plasma proteome has so far hampered the identification of such low abundant markers. To overcome this challenge we analyzed the plasma microparticle proteome, and reached an unprecedented depth of over 3000 plasma proteins in single runs. To add a quantitative dimension, we developed PROMIS-Quan-PROteomics of MIcroparticles with Super-Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) Quantification, a novel mass spectrometry-based technology for plasma microparticle proteome quantification. PROMIS-Quan enables a two-step relative and absolute SILAC quantification. First, plasma microparticle proteomes are quantified relative to a super-SILAC mix composed of cell lines from distinct origins. Next, the absolute amounts of selected proteins of interest are quantified relative to the super-SILAC mix. We applied PROMIS-Quan to prostate cancer and compared plasma microparticle samples of healthy individuals and prostate cancer patients. We identified in total 5374 plasma-microparticle proteins, and revealed a predictive signature of three proteins that were elevated in the patient-derived plasma microparticles. Finally, PROMIS-Quan enabled determination of the absolute quantitative changes in prostate specific antigen (PSA) upon treatment. We propose PROMIS-Quan as an innovative platform for biomarker discovery, validation, and quantification in both the biomedical research and in the clinical worlds.
authors.affiliation: From the ‡Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel;
authors.forename: Michal
authors.initials: M
authors.lastname: Harel
authors.affiliation: §Department of Molecular Pharmacology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa, Israel;
authors.forename: Pazit
authors.initials: P
authors.lastname: Oren-Giladi
authors.affiliation: ¶Division of Oncology, Rambam Health Care Campus, Haifa, Israel.
authors.forename: Orit
authors.initials: O
authors.lastname: Kaidar-Person
authors.affiliation: §Department of Molecular Pharmacology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa, Israel;
authors.forename: Yuval
authors.initials: Y
authors.lastname: Shaked
authors.affiliation: From the ‡Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; geiger@post.tau.ac.il.
authors.forename: Tamar
authors.initials: T
authors.lastname: Geiger
mesh_terms: D000596:Amino Acids / Q000378:metabolism*; D015415:Biomarkers / Q000097:blood*; D001798:Blood Proteins / Q000378:metabolism; D018929:Cell Culture Techniques; D055252:Cell-Derived Microparticles / Q000378:metabolism*; D006801:Humans; D007553:Isotope Labeling / Q000379:methods*; D008297:Male; D011471:Prostatic Neoplasms / Q000097:blood / Q000378:metabolism; D020543:Proteome / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D012015:Reference Standards; D015203:Reproducibility of Results
chemical_list: D000596:Amino Acids; D015415:Biomarkers; D001798:Blood Proteins; D020543:Proteome