Comparison of serum fractionation methods by data independent label-free proteomics

•Five prefractionation methods were compared with initial raw serum using data independent label-free analysis.•Not all the commercial prefractionation methods tested show the expected efficiency on serum.•The ProteoPrep® 20 enabled a 49% increase in the number of protein identifications.•The ProteoPrep® 20 reached proteins at initial raw serum concentration 61 times lower than what was obtained for the raw serum.•Qualitative and quantitative data (including repeatability and recovery) are discussed for clinical proteomics application.

Off-line sample prefractionations applied prior to biomarker discovery proteomics are options to enable more protein identifications and detect low-abundance proteins. This work compared five commercial methods efficiency to raw serum analysis using label-free proteomics. The variability of the protein quantities determined for each process was similar to the unprefractionated serum. A 49% increase in protein identifications and 12.2% of reliable quantification were obtained. A 61 times lower limit of protein quantitation was reached compared to protein concentrations observed in raw serum. The concentrations of detected proteins were confronted to estimated reference values.

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