Diao Lixia, Clarke Charlotte H, Coombes Kevin R, Hamilton Stanley R, Roth Jack, Mao Li, Czerniak Bogdan, Baggerly Keith A, Morris Jeffrey S, Fung Eric T, Bast Robert C
Departments of Bioinformatics and Computational Biology.
Cancer Inform. 2011 Mar 14;10:45-64. doi: 10.4137/CIN.S6438.
This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited.The reproducibility of mass spectrometry (MS) data collected using surface enhanced laser desorption/ionization-time of flight (SELDI-TOF) has been questioned. This investigation was designed to test the reproducibility of SELDI data collected over time by multiple users and instruments. Five laboratories prepared arrays once every week for six weeks. Spectra were collected on separate instruments in the individual laboratories. Additionally, all of the arrays produced each week were rescanned on a single instrument in one laboratory. Lab-to-lab and array-to-array variability in alignment parameters were larger than the variability attributable to running samples during different weeks. The coefficient of variance (CV) in spectrum intensity ranged from 25% at baseline, to 80% in the matrix noise region, to about 50% during the exponential drop from the maximum matrix noise. Before normalization, the median CV of the peak heights was 72% and reduced to about 20% after normalization. Additionally, for the spectra from a common instrument, the CV ranged from 5% at baseline, to 50% in the matrix noise region, to 20% during the drop from the maximum matrix noise. Normalization reduced the variability in peak heights to about 18%. With proper processing methods, SELDI instruments produce spectra containing large numbers of reproducibly located peaks, with consistent heights.
这是一篇开放获取文章。只要对原始作品进行恰当引用，允许不受限制的非商业用途。使用表面增强激光解吸/电离飞行时间质谱（SELDI-TOF）收集的质谱（MS）数据的可重复性受到了质疑。本研究旨在测试多个用户和仪器随时间收集的SELDI数据的可重复性。五个实验室连续六周每周制备一次芯片。在各个实验室的单独仪器上收集光谱。此外，每周生产的所有芯片都在一个实验室的一台仪器上重新扫描。实验室间和芯片间校准参数的变异性大于不同周运行样品所导致的变异性。光谱强度的变异系数（CV）在基线时为25%，在基质噪声区域为80%，在从最大基质噪声呈指数下降期间约为50%。在归一化之前，峰高的中位数CV为72%，归一化后降至约20%。此外，对于来自同一仪器的光谱，CV在基线时为5%，在基质噪声区域为50%，在从最大基质噪声下降期间为20%。归一化将峰高的变异性降低到约18%。通过适当的处理方法，SELDI仪器产生的光谱包含大量可重复定位的峰，且峰高一致。
