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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