Received on May 15, 2004
Accepted on October 22, 2004

Proteomics and Protein Markers

Enhancement of Sensitivity and Resolution of Surface-Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometric Records for Serum Peptides Using Time-Series Analysis Techniques

¹ Departments of Applied Science, Physics, and Mathematics, the College of William and Mary, Williamsburg, VA, and Applied Science, and INCOGEN, Inc., Williamsburg, VA
² Departments of Applied Science, Physics, and Mathematics, the College of William and Mary, Williamsburg, VA, and Physics
³ Departments of Applied Science, Physics, and Mathematics, the College of William and Mary, Williamsburg, VA, and Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, and Current affiliation: Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta, GA 30912
⁴ Departments of Applied Science, Physics, and Mathematics, the College of William and Mary, Williamsburg, VA, and Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA
⁵ Departments of Applied Science, Physics, and Mathematics, the College of William and Mary, Williamsburg, VA, and Physics, and INCOGEN, Inc., Williamsburg, VA
⁶ Departments of Applied Science, Physics, and Mathematics, the College of William and Mary, Williamsburg, VA, and Physics, the College of William and Mary, Williamsburg, VA
⁷ Departments of Applied Science, Physics, and Mathematics, the College of William and Mary, Williamsburg, VA, and Mathematics, the College of William and Mary, Williamsburg, VA
⁸ Departments of Applied Science, Physics, and Mathematics, the College of William and Mary, Williamsburg, VA, and INCOGEN, Inc., Williamsburg, VA
⁹ Departments of Applied Science, Physics, and Mathematics, the College of William and Mary, Williamsburg, VA, and Applied Science, and Physics, the College of William and Mary, Williamsburg, VA

^* To whom correspondence should be addressed. E-mail: dasha{at}compsci.wm.edu.

Background: 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.

Methods: 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.

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.