"Cheek-to-cheek" urinary proteome profiling via combinatorial peptide ligand libraries: A novel, unexpected elution system

Giovanni Candiano, Laura Santucci, Maurizio Bruschi, Andrea Petretto, Chiara D. Ambrosio, Andrea Scaloni, Pier Giorgio Righetti, Gian Marco Ghiggeri

Research output: Contribution to journalArticlepeer-review


A new method is here reported for facile elution of the human urinary proteome after being captured with combinatorial peptide ligand libraries (CPLL, ProteoMiner). It consists in challenging the beads with 100. mM Tris, pH 7.4, or with 100. mM Lys, pH 7.4 or even better with a mixture of Lys, Arg, Asp and Glu (150. mM final concentration). These elutions permit recovery of species in a native form, for monitoring any biological activity of the eluted species, while avoiding the noxious presence of sodium dodecyl sulphate (SDS), reported as the best eluant so far from CPLL beads. SDS, albeit permitting quantitative recovery from the beads, has to be removed from the sample prior to mass spectrometry analysis. This unorthodox elution, which most likely will work only for urine samples, seems to be due to the fact that bile salts and urinary pigments are massively adsorbed by the beads, thus masking the hydrophobic binding sites of aromatic and non-aromatic amino acids. The binding thus occurs mostly via ionic and hydrogen bond interactions via the "Grand Catchers" Arg, Lys, His, which can then be easily challenged by positively charged species, such a Tris, free Lys and free Arg in the eluant as well as by negatively charged compounds, such as Glu and Asp. When eluting with the four-amino acid mix, at least 3300 spots can be visualized in a 2D map.

Original languageEnglish
Pages (from-to)796-805
Number of pages10
JournalJournal of Proteomics
Issue number3
Publication statusPublished - Jan 4 2012


  • Biomarkers
  • Combinatorial peptide libraries
  • Human urine
  • Low-abundance proteins
  • Proteomics

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics


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