Comparing the old and new generation SELDI-TOF MS: implications for serum protein profiling

Abstract

Background: Although the PBS-IIc SELDI-TOF MS apparatus has been extensively used in the search for better biomarkers, issues have been raised concerning the semi-quantitative nature of the technique and its reproducibility. To overcome these limitations, a new SELDI-TOF MS instrument has been introduced: the PCS 4000 series. Changes in this apparatus compared to the older one are a.o. an increased dynamic range of the detector, an adjusted configuration of the detector sensitivity, a raster scan that ensures more complete desorption coverage and an improved detector attenuation mechanism. In the current study, we evaluated the performance of the old PBS-IIc and new PCS 4000 series generation SELDI-TOF MS apparatus.

Methods: To this end, two different sample sets were profiled after which the same ProteinChip arrays were analysed successively by both instruments. Generated spectra were analysed by the associated software packages. The performance of both instruments was evaluated by assessment of the number of peaks detected in the two sample sets, the biomarker potential and reproducibility of generated peak clusters, and the number of peaks detected following serum fractionation.

Results: We could not confirm the claimed improved performance of the new PCS 4000 instrument, as assessed by the number of peaks detected, the biomarker potential and the reproducibility. However, the PCS 4000 instrument did prove to be of superior performance in peak detection following profiling of serum fractions.

Conclusion: As serum fractionation facilitates detection of low abundant proteins through reduction of the dynamic range of serum proteins, it is now increasingly applied in the search for new potential biomarkers. Hence, although the new PCS 4000 instrument did not differ from the old PBS-IIc apparatus in the analysis of crude serum, its superior performance after serum fractionation does hold promise for improved biomarker detection and identification.

Figure 1

Plots of Spearman's rank correlation coefficient and p-values for all peaks detected in the BC data sets. Depicted are the mean (red) and median (black) values of all peaks detected in the three data sets of the BC sample set. PBS: data set 1a (PBS-IIc generated data, analysed by ProteinChip software), PCS: data set 2 (PCS 4000 generated data, analysed by Ciphergen Express™), PBS/PCS: data set 1b (PBS-IIc generated data, analysed by Ciphergen Express™).

Figure 2

Plots of Spearman's rank correlation coefficient and p-values for common peaks detected in the BC data sets. Depicted are the mean (red) and median (black) values of common peaks detected across all three data sets of the BC sample set. PBS: data set 1a (PBS-IIc generated data, analysed by ProteinChip software), PCS: data set 2 (PCS 4000 generated data, analysed by Ciphergen Express™), PBS/PCS: data set 1b (PBS-IIc generated data, analysed by Ciphergen Express™).

Figure 3

Spectra of serum fractions analysed on CM10 arrays and measured on the PBS-IIc and PCS 4000 instrument. A: flow through/pH 9 fractions, B: pH 7 fractions.