Gast Marie-Christine W, Engwegen Judith Ymn, Schellens Jan Hm, Beijnen Jos H
Department of Pharmacy & Pharmacology, The Netherlands Cancer Institute/Slotervaart Hospital, Amsterdam, The Netherlands.
BMC Med Genomics. 2008 Jan 31;1:4. doi: 10.1186/1755-8794-1-4.
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.
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.
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.
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.
尽管PBS-IIc表面增强激光解吸/电离飞行时间质谱仪（SELDI-TOF MS）已被广泛用于寻找更好的生物标志物，但该技术的半定量性质及其可重复性引发了一些问题。为克服这些局限性，一种新型的SELDI-TOF MS仪器已被推出：PCS 4000系列。与旧仪器相比，该仪器的变化包括探测器动态范围增加、探测器灵敏度配置调整、光栅扫描确保更完全的解吸覆盖以及改进的探测器衰减机制。在本研究中，我们评估了旧的PBS-IIc和新的PCS 4000系列SELDI-TOF MS仪器的性能。
为此，对两组不同的样本进行分析，然后两台仪器依次分析相同的蛋白质芯片阵列。生成的光谱由相关软件包进行分析。通过评估在两组样本中检测到的峰数量、生物标志物潜力和生成的峰簇的可重复性，以及血清分级分离后检测到的峰数量，来评估两台仪器的性能。
通过检测到的峰数量、生物标志物潜力和可重复性评估，我们无法证实新的PCS 4000仪器所宣称的性能提升。然而，在血清分级分析后的峰检测中，PCS 4000仪器确实表现出卓越的性能。
由于血清分级通过降低血清蛋白的动态范围有助于检测低丰度蛋白，它现在越来越多地应用于寻找新的潜在生物标志物。因此，尽管新的PCS 4000仪器在粗血清分析中与旧的PBS-IIc仪器没有差异，但其在血清分级后的卓越性能确实有望改善生物标志物的检测和鉴定。
