Comparison of Two Solid-Phase Extraction (SPE) Methods for the Identification and Quantification of Porcine Retinal Protein Markers by LC-MS/MS

Proper sample preparation protocols represent a critical step for liquid chromatography-mass spectrometry (LC-MS)-based proteomic study designs and influence the speed, performance and automation of high-throughput data acquisition. The main objective of this study was to compare two commercial solid-phase extraction (SPE)-based sample preparation protocols (comprising SOLA mu (TM) HRP SPE spin plates from Thermo Fisher Scientific and ZIPTIP (R) C18 pipette tips from Merck Millipore) for analytical performance, reproducibility, and analysis speed. The house swine represents a promising animal model for studying human eye diseases including glaucoma and provides excellent requirements for the qualitative and quantitative MS-based comparison in terms of ocular proteomics. In total six technical replicates of two protein fractions [extracted with 0.1% dodecyl-ss-maltoside (DDM) or 1% trifluoroacetic acid (TFA)] of porcine retinal tissues were subjected to in-gel trypsin digestion and purified with both SPE-based workflows (N = 3) prior to LC-MS analysis. On average, 550 +/- 70 proteins (1512 +/- 199 peptides) and 305 +/- 48 proteins (806 +/- 144 peptides) were identified from DDM and TFA protein fractions, respectively, after ZIPTIP (R) C18 purification, and SOLA mu (TM) workflow resulted in the detection of 513 +/- 55 proteins (1347 +/- 180 peptides) and 300 +/- 33 proteins (722 +/- 87 peptides), respectively (FDR < 1%). Venn diagram analysis revealed an average overlap of 65 +/- 2% (DDM fraction) and 69 +/- 4% (TFA fraction) in protein identifications between both SPE-based methods. Quantitative analysis of 25 glaucoma-related protein markers also showed no significant differences (P > 0.05) regarding protein recovery between both SPE methods. However, only glaucoma-associated marker MECP2 showed a significant (P = 0.02) higher abundance in ZIPTIP (R)-purified replicates in comparison to SOLA mu (TM)-treated study samples. Nevertheless, this result was not confirmed in the verification experiment using in-gel trypsin digestion of recombinant MECP2 (P = 0.24). In conclusion, both SPE-based purification methods worked equally well in terms of analytical performance and reproducibility, whereas the analysis speed and the semi-automation of the SOLA mu (TM) spin plates workflow is much more convenient in comparison to the ZIPTIP (R) C18 method.