Comparison of diverse affinity based high-abundance protein depletion strategies for improved bio-marker discovery in oral fluids

Guy Krief, Omer Deutsch, Batia Zaks, David T. Wong, Doron J. Aframian, Aaron Palmon*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

21 Scopus citations


Oral fluids (OF) have been suggested as a source of biomarkers for oral and systemic health, but as with other bio-fluids, the presence of high-abundance proteins interferes with the detection of lower-abundance biomarkers. Here, we compared the performance of four depletion treatments: triple depletion (TD) of amylases, albumins and immunoglobulin G; multiple depletion (MD) of amylases and a panel of 20 proteins, a combination of the two (EMD) and combinatorial peptide ligand library based depletion termed CPLL. TD, MD, EMD and CPLL removed 76%, 83%, 85% and 94% of total proteins, respectively, coupled with increased low abundance protein detection and narrowed dynamic range. 2-DE revealed that all depletion pretreatments successfully clarified areas hampered by high-abundance proteins; however, EMD and CPLL exposed the highest number of proteins. Quantitative MS of EMD samples relative to none treated samples indicated that most of downregulated proteins (> 90%) were EMD target proteins. In conclusion, a multiple step EMD and CPLL depletion approaches bring about the highest number of protein detection ability and the best hampered-area clearance. As CPLL requires at least 10 fold more protein starting material, we suggest EMD pretreatment as a new detection tool in instances of low protein starting material.

Original languageAmerican English
Pages (from-to)4165-4175
Number of pages11
JournalJournal of Proteomics
Issue number13
StatePublished - 16 Jul 2012

Bibliographical note

Funding Information:
This research was supported by the US-Israel Binational Science Foundation grant no. 2009294 . MS identification by Smoler Proteomics Center at the Technion.


  • Low abundance proteins
  • Oral fluid
  • Protein depletion
  • Quantitative proteomics
  • Saliva biomarker


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