Comparative evaluation of peptide desalting methods for salivary proteome analysis
Nico Jehmlich1, Claas Golatowski1, Annette Murr1
1Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Germany.
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.
Material And 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.
Conclusion:
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.
