title: Comparative evaluation of peptide desalting methods for salivary proteome analysis.
abstract: BACKGROUND
  Reliability and reproducibility are common requirements for high-quality generation of proteome data using mass spectrometry. The aim of this study was to compare four single-step desalting devices to provide a reproducible, high-recovery method for concentrating and purifying tryptic peptides before LC-MS/MS measurements.
  
  
  METHODS
  Four different methods for peptide purification prior LC-MS/MS analyses (μC18 ZipTip® pipette tips, C18 ZipTip® pipette tips, TopTip C-18 and OASIS® HLB μElution Plate) were tested using whole saliva from healthy volunteers. A number of protein identifications and salivary protein patterns were analyzed comparatively.
  
  
  RESULTS
  Each desalting device facilitated the identification of about 340 proteins. Purification-method dependent variations in protein composition were observed. Nevertheless, the overall inter-approach Pearson correlation coefficients of >0.95 indicate high reproducibility, reliability and recovery of proteins.
  
  
  CONCLUSIONS
  The applied devices performed equally well in the removal of low molecular weight contaminants and provide high-quality data for quantitative proteomic analysis. Thus, selection should be primarily based on the amount of peptide extract available and the number of samples to be processed.
authors.affiliation: Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Germany. Electronic address: nico.jehmlich@ufz.de.
authors.forename: Nico
authors.initials: N
authors.lastname: Jehmlich
authors.affiliation: Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Germany. Electronic address: claas@golatowski.de.
authors.forename: Claas
authors.initials: C
authors.lastname: Golatowski
authors.affiliation: Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Germany. Electronic address: annette.murr@uni-greifswald.de.
authors.forename: Annette
authors.initials: A
authors.lastname: Murr
authors.affiliation: Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Germany. Electronic address: gesell@uni-greifswald.de.
authors.forename: Gesell
authors.initials: G
authors.lastname: Salazar
authors.affiliation: Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Germany. Electronic address: dhoplevm@uni-greifswald.de.
authors.forename: Vishnu Mukund
authors.initials: VM
authors.lastname: Dhople
authors.affiliation: Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Germany. Electronic address: hammer@uni-greifswald.de.
authors.forename: Elke
authors.initials: E
authors.lastname: Hammer
authors.affiliation: Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Germany. Electronic address: voelker@uni-greifswald.de.
authors.forename: Uwe
authors.initials: U
authors.lastname: Völker
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods; D006801:Humans; D010455:Peptides / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012463:Saliva / Q000737:chemistry*; D012680:Sensitivity and Specificity; D053719:Tandem Mass Spectrometry
chemical_list: D010455:Peptides
keywords: Peptide desalting devices; Peptide purification; Saliva proteomics; Shotgun LC–MS/MS