Comparative evaluation of peptide desalting methods for salivary proteome analysis

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.