Proteomics of microparticles with SILAC quantification (PROMIS-Quan): A novel proteomic method for plasma biomarker quantification

Michal Harel, Pazit Oren-Giladi, Orit Kaidar-Person, Yuval Shaked, Tamar Geiger*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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, PROMISQuan 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.

Original languageEnglish
Pages (from-to)1127-1136
Number of pages10
JournalMolecular and Cellular Proteomics
Volume14
Issue number4
DOIs
StatePublished - 1 Apr 2015

Funding

FundersFunder number
Israel Science Foundation1617/12

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