title: High abundance proteins depletion vs low abundance proteins enrichment: comparison of methods to reduce the plasma proteome complexity.
abstract: BACKGROUND
  To date, the complexity of the plasma proteome exceeds the analytical capacity of conventional approaches to isolate lower abundance proteins that may prove to be informative biomarkers. Only complex multistep separation strategies have been able to detect a substantial number of low abundance proteins (<100 ng/ml). The first step of these protocols is generally the depletion of high abundance proteins by the use of immunoaffinity columns or, alternatively, the enrichment of by the use of solid phase hexapeptides ligand libraries.
  
  
  RESULTS
  Here we present a direct comparison of these two approaches. Following either approach, the plasma sample was further fractionated by SCX chromatography and analyzed by RP-LC-MS/MS with a Q-TOF mass spectrometer. The depletion of the 20 most abundant plasma proteins allowed the identification of about 25% more proteins than those detectable following low abundance proteins enrichment. The two datasets are partially overlapping and the identified proteins belong to the same order of magnitude in terms of plasma concentration.
  
  
  CONCLUSIONS
  Our results show that the two approaches give complementary results. However, the enrichment of low abundance proteins has the great advantage of obtaining much larger amount of material that can be used for further fractionations and analyses and emerges also as a cheaper and technically simpler approach. Collectively, these data indicate that the enrichment approach seems more suitable as the first stage of a complex multi-step fractionation protocol.
authors.affiliation: Department of Clinical and Experimental Medicine, Division of Metabolism, University of Padua, Padua, Italy. millionirenato@gmail.com
authors.forename: Renato
authors.initials: R
authors.lastname: Millioni
authors.forename: Serena
authors.initials: S
authors.lastname: Tolin
authors.forename: Lucia
authors.initials: L
authors.lastname: Puricelli
authors.forename: Stefano
authors.initials: S
authors.lastname: Sbrignadello
authors.forename: Gian Paolo
authors.initials: GP
authors.lastname: Fadini
authors.forename: Paolo
authors.initials: P
authors.lastname: Tessari
authors.forename: Giorgio
authors.initials: G
authors.lastname: Arrigoni
mesh_terms: D001798:Blood Proteins / Q000032:analysis*; D005591:Chemical Fractionation; D016001:Confidence Intervals; D006801:Humans; D010455:Peptides / Q000097:blood; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000191:economics / Q000379:methods*
chemical_list: D001798:Blood Proteins; D010455:Peptides; D020543:Proteome