Malyarenko Dariya I, Cooke William E, Adam Bao-Ling, Malik Gunjan, Chen Haijian, Tracy Eugene R, Trosset Michael W, Sasinowski Maciek, Semmes O John, Manos Dennis M
Departments of Applied Science, the College of William and Mary, Williamsburg, VA 23187-8795, USA.
Clin Chem. 2005 Jan;51(1):65-74. doi: 10.1373/clinchem.2004.037283. Epub 2004 Nov 18.
Measurement of peptide/protein concentrations in biological samples for biomarker discovery commonly uses high-sensitivity mass spectrometers with a surface-processing procedure to concentrate the important peptides. These time-of-flight (TOF) instruments typically have low mass resolution and considerable electronic noise associated with their detectors. The net result is unnecessary overlapping of peaks, apparent mass jitter, and difficulty in distinguishing mass peaks from background noise. Many of these effects can be reduced by processing the signal using standard time-series background subtraction, calibration, and filtering techniques.
Surface-enhanced laser desorption/ionization (SELDI) spectra were acquired on a PBS II instrument from blank, hydrophobic, and IMAC-Cu ProteinChip arrays (Ciphergen Biosystems, Inc.) incubated with calibration peptide mixtures or pooled serum. TOF data were recorded after single and multiple laser shots at different positions. Correlative analysis was used for time-series calibration. Target filters were used to suppress noise and enhance resolution after baseline removal and noise rescaling.
The developed algorithms compensated for the electronic noise attributable to detector overload, removed the baseline caused by charge accumulation, detected and corrected mass peak jitter, enhanced signal amplitude at higher masses, and improved the resolution by using a deconvolution filter.
These time-series techniques, when applied to SELDI-TOF data before any peak identification procedure, can improve the data to make the peak identification process simpler and more robust. These improvements may be applicable to most TOF instrumentation that uses analog (rather than counting) detectors.
在生物标志物发现中，测量生物样品中的肽/蛋白质浓度通常使用具有表面处理程序的高灵敏度质谱仪来浓缩重要肽段。这些飞行时间（TOF）仪器通常具有低质量分辨率，并且其检测器存在相当大的电子噪声。最终结果是峰不必要的重叠、明显的质量抖动以及难以将质量峰与背景噪声区分开来。通过使用标准的时间序列背景扣除、校准和滤波技术处理信号，可以减少许多这些影响。
在PBS II仪器上，从与校准肽混合物或混合血清孵育的空白、疏水和IMAC-Cu蛋白质芯片阵列（Ciphergen Biosystems公司）获取表面增强激光解吸/电离（SELDI）光谱。在不同位置进行单次和多次激光照射后记录TOF数据。使用相关分析进行时间序列校准。在基线去除和噪声重新缩放后，使用目标滤波器抑制噪声并提高分辨率。
所开发的算法补偿了由于检测器过载引起的电子噪声，去除了电荷积累导致的基线，检测并校正了质量峰抖动，增强了较高质量处的信号幅度，并通过使用反卷积滤波器提高了分辨率。
在任何峰识别程序之前将这些时间序列技术应用于SELDI-TOF数据，可以改善数据，使峰识别过程更简单、更稳健。这些改进可能适用于大多数使用模拟（而非计数）检测器的TOF仪器。
