title: A cost-effective method to get insight into the peritoneal dialysate effluent proteome.
abstract: Protein depletion with acetonitrile and protein equalization with dithiothreitol have been assessed with success as proteomics tools for getting insight into the peritoneal dialysate effluent proteome. The methods proposed are cost-effective, fast and easy of handling, and they match the criteria of analytical minimalism: low sample volume and low reagent consumption. Using two-dimensional gel electrophoresis and peptide mass fingerprinting, a total of 72 unique proteins were identified. Acetonitrile depletes de PDE proteome from high-abundance proteins, such as albumin, and enriches the sample in apolipo-like proteins. Dithiothreitol equalizes the PDE proteome by diminishing the levels of albumin and enriching the extract in immunoglobulin-like proteins. The annotation per gene ontology term reveals the same biological paths being affected for patients undergoing peritoneal dialysis, namely that the largest number of proteins lost through peritoneal dialysate are extracellular proteins involved in regulation processes through binding.
  
  
  
  Renal failure is a growing problem worldwide, and particularly in Europe where the population is getting older. 
  
  Up-to-date there is a focus of interest in peritoneal dialysis (PD), as it provides a better quality of life and autonomy of the patients than other renal replacement therapies such as haemodialysis. However, PD can only be used during a short period of years, as the peritoneum lost its permeability through time. Therefore to make a breakthrough in PD and consequently contribute to better healthcare system it is urgent to find a group of biomarkers of peritoneum degradation. 
  
  Here we report on two cost-effective methods for protein depletion in peritoneal dialysate effluent (PDE). The use of ACN and DTT over PDE to deplete high abundant proteins or to equalize the concentration of proteins, respectively, performs well and with similar protein profiles than when the same chemicals are used in human plasma samples. 
  
  ACN depletes de PDE proteome from large proteins, such as albumin, and enriches the sample in apolipoproteins. 
  
  DTT equalizes the PDE proteome by diminishing the levels of large proteins such as albumin and enriching the extract in immunoglobulins. 
  
  Although the number and type of proteins identified are different, the annotation per gene ontology term reveals the same biological paths being affected for patients undergoing peritoneal dialysate. Thus, the largest number of proteins lost through peritoneal dialysate belongs to the group of extracellular proteins involved in regulation processes through binding. As for the searching of biomarkers, DTT seems to be the most promising of the two methods because acts as an equalizer and it allows interrogating more proteins in the same sample.
authors.affiliation: UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Bioscope Research Group, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; ProteoMass Scientific Society, Madan Park, Rua dos Inventores, 2825-152 Caparica, Portugal.
authors.forename: J E
authors.initials: JE
authors.lastname: Araújo
authors.affiliation: UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Bioscope Research Group, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; ProteoMass Scientific Society, Madan Park, Rua dos Inventores, 2825-152 Caparica, Portugal.
authors.forename: S
authors.initials: S
authors.lastname: Jorge
authors.affiliation: Nephrology Department, Hospital Garcia de Orta, Almada, Portugal.
authors.forename: F
authors.initials: F
authors.lastname: Teixeira E Costa
authors.affiliation: Nephrology Department, Hospital Garcia de Orta, Almada, Portugal.
authors.forename: A
authors.initials: A
authors.lastname: Ramos
authors.affiliation: UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Bioscope Research Group, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; ProteoMass Scientific Society, Madan Park, Rua dos Inventores, 2825-152 Caparica, Portugal.
authors.forename: C
authors.initials: C
authors.lastname: Lodeiro
authors.affiliation: UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Bioscope Research Group, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; ProteoMass Scientific Society, Madan Park, Rua dos Inventores, 2825-152 Caparica, Portugal. Electronic address: hmsantos@fct.unl.pt.
authors.forename: H M
authors.initials: HM
authors.lastname: Santos
authors.affiliation: UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Bioscope Research Group, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; ProteoMass Scientific Society, Madan Park, Rua dos Inventores, 2825-152 Caparica, Portugal. Electronic address: jlcm@fct.unl.pt.
authors.forename: J L
authors.initials: JL
authors.lastname: Capelo
mesh_terms: D000097:Acetonitriles; D015415:Biomarkers; D004229:Dithiothreitol; D015180:Electrophoresis, Gel, Two-Dimensional; D006801:Humans; D013058:Mass Spectrometry; D010530:Peritoneal Dialysis / Q000592:standards*; D010537:Peritoneum / Q000378:metabolism; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000191:economics / Q000379:methods
chemical_list: D000097:Acetonitriles; D015415:Biomarkers; D020543:Proteome; D004229:Dithiothreitol; C032159:acetonitrile
keywords: Acetonitrile; Dithiothreitol; High-abundance proteins; Peritoneal dialysis effluent; Protein depletion; Sample preparation; and Proteomics