Enhancement of sensitivity and resolution of surface-enhanced, laser desorption/lonization time-of-flight mass spectrometric records for serum peptides using time-series analysis techniques

Background: Measurement of peptide/protein concentrations in biological samples for biomarker discovery commonly uses high-sensitivity mass spectrometers with a surf ace-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 timeseries background subtraction, calibration, and filtering techniques. Methods: Surface-enhanced laser desorption/ionization (SELDI) spectra were acquired on a PBS II instrument from blank, hydrophobic, and IMAC-Cu ProteinChip((R)) 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. Results: 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. Conclusions: 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. (C) 2005 American Association for Clinical Chemistry.