0132 : Usefulness of multiple proteinchip arrays for proteomic profiling using surface enhanced laser desorption ionization – time of flight – mass spectrometry (SELDI-TOF-MS)

Abstract

Multiple proteinchip arrays have been developed to selectively bind proteins with diverse physical and chemical properties before the profiling step with SELDI-TOF-MS. However, the additional value of each array is poorly described. A proteomic analysis has been performed in plasma of 198 patients with chronic heart failure with a left ventricular ejection fraction <45%. Plasma samples were profiled with CM10 (Weak Cation Exchanger) and H50 (Hydrophobic) proteinchip arrays in a PBS 4000 SELDI-TOF-MS (BioRad Laboratories). To ensure sufficient coverage of the entire mass range, the acquisition settings for low-mass (LM, 2500-30000 Da) and high-mass (HM, >20000 Da) m/z peaks were optimized separately. Correlation between peaks was analysed face to face by the test of Pearson. We detected 203m/z peaks: 109 (52 LM and 42 HM) peaks with the CM10 array and 94 (69 LM and 40 HM) peaks with the H50 array. Among the peaks detected on the H50 array, 28 LM and 8 HM peaks were also present on the CM10 array. In the mass range 20000-30000 Da, peaks can be detected with both, LM and HM acquisition settings. We found 6 of the 13 HM peaks on the CM10 array and 7 of the 15 HM peaks on the H50 array also detected with LM settings. 093We then analysed the correlation among the 203m/z peaks detected with both types of arrays. We found that 56 (27.5%) peaks were highly correlated with at least one other peak with a correlation coefficient r>0.9. Altogether, 30 out of these 56 peaks were correlated with 1 other peak, 14 with 2 other peaks, 7 with 3, 3 with 4, 1 with 5 and 1 with 6 other peaks. These highly correlated peaks may correspond to a unique protein. Profiling with multiple proteinchip arrays provides data with high redundancy and colinearity. This finding may be useful for chosen the SELDITOF- MS peaks to be purified and identified. In addition, a unique array (CM10) may be sufficient to obtain a relevant profiling of plasma proteins.