Combinatorial Peptide Ligand Library and two dimensional electrophoresis: New frontiers in the study of peritoneal dialysis effluent in pediatric patients

Effects of Alanyl-Glutamine Treatment on the Peritoneal Dialysis Effluent Proteome Reveal Pathomechanism-Associated Molecular Signatures

“…Despite these obvious investigational benefits of PDE, current strategies of proteomic analysis of soluble PDE proteins in cell-free PDE have typically been compromised by the high dynamic range of protein concentrations, resembling a plasma-like composition with several high abundance proteins. Because of the employed analytical techniques, these challenges have limited previously reported proteomic analyses of PDE to identification of only 171 unique proteins, most of which are high-abundance plasma proteins ( 7 – 19 ).…”

“…Although the precise mechanism of binding has been disputed ( 43 ), we have shown for low abundance proteins that the CPLL procedure influences quantitation to a lesser extent ( 20 ). It should be noted, that a suboptimal bead-to-PDE ratio, by which high abundance proteins are insufficiently removed by the CPLL beads, or the use of insensitive downstream methods still results in loss of low abundance proteins ( 8 , 19 ). The second workflow component is therefore the application of highly accurate methods of separation, detection and quantitation, including use of sensitive fluorescent dyes in gels and isobaric tags in LC-MS for efficient and quantitative comparison of PDE samples.…”

“…A literature search in NCBI Pubmed utilizing the query string (proteomics AND peritoneal dialysis) OR (proteome AND peritoneal dialysis) OR (proteomics AND peritoneal fluid) OR (proteome AND peritoneal fluid) OR (proteomics AND peritoneal effluent) OR (proteome AND peritoneal effluent) on Oct 26, 2017 resulted in 83 hits. These were restricted to clinical peritoneal dialysis effluent from humans, to return only 15 studies ( 7 – 19 , 38 , 39 ) of which two were excluded because they focused solely on the exosomal fraction ( 38 , 39 ) and one did not provide any protein accessions ( 19 ), resulting in 12 studies and 171 unique proteins for analysis ( supplemental Table S1 ) ( 7 – 18 ). Manual query of protein names presented by Zavvos et al ( 19 ) yielded 19 protein names not contained in the 171, of which 11 were unreviewed and 8 were reviewed entries in UniProt.…”

“…Nevertheless, previous proteomic efforts to develop novel PDE biomarkers have been hindered by the PDE's plasma-like dynamic range of protein abundances, by the limited performance of separation and detection techniques applied to date, and by the design of the clinical trials from which the PDE samples were obtained. Thirteen published proteomic analyses of soluble PDE proteins have to date identified 171 unique proteins ( 7 – 19 ).…”

A prospective, proteomics study identified potential biomarkers of encapsulating peritoneal sclerosis in peritoneal effluent

“…Peritoneal dialysis effluent (PDE) biomarkers that could predict the onset or confirm the diagnosis of EPS would allow the development of prognostic tools and, potentially , the identification of future therapeutic targets. Proteomics technologies provide us with powerful tools for an in-depth exploration of the PDE proteome, yet relevant studies have been few and to date preliminary (22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38) .…”