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Norfolk

Norfolk. Enhancement of Sensitivity and Resolution of SELDI-TOF MS records. ENAR 03/05. W&M, INCOGEN, EVMS Collaboration. Hardware Issues. Performance Enhancement Tools. SELDI Profiling: Sources of Error. +. +. +. S ij. source and detector related: D S ij , D j ( D M/z).

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Norfolk

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  1. Norfolk Enhancement of Sensitivity and Resolution of SELDI-TOF MS records ENAR 03/05 W&M, INCOGEN, EVMS Collaboration Hardware Issues Performance Enhancement Tools

  2. SELDI Profiling: Sources of Error + + + Sij source and detector related: DSij, Dj (DM/z)

  3. H. Chen 03/23, 11:45 Sij Typical VIBE-MS Analysis Pipeline

  4. Enhancing Data Quality ApoAI+H+ +SA +2SA +3SA characterizing uncertainties… • Relevance (protein?): noise vs. signal characteristics • Location (Dj?): alignment, deconvolution • Intensity (DSij?): baseline, resampling, deconvolution

  5. Comprehensive Data Survey

  6. Hardware Settings

  7. SELDI Surface Evolution 0 shots 20 shots 200 shots 500 mm EVMS Acquisition Protocol 8 kDa 10 kDa 6 kDa • Acquisition • requires • optimization • TOF to M/z • calibration • may vary • Process • individual • shots

  8. Overload Baseline • Length is proportional to the number of overload points • Single shot correction only

  9. Charge Accumulation Baseline • Baseline is predictable from 3-parameter RC-modeling (Clin.Chem.2005, 51: 65-74) • Single shot or average

  10. Peak Alignment Between Spots QC record # • Detect shifts in time • Align in time Time point

  11. TOF-Jitter Within Spot • TOF and intensity varies due to surface roughness DTOF = 2 ns/mm (2 mm/dwell period) +/-10 mm  +/-5 time points

  12. Subposition De-Jittering • Correct by subposition de-jittering during acquisition • Gain resolution (even from only 12 subpositions)

  13. Deconvolution With Shaping Filter shaping W -1 denoising W deconvolution

  14. SELDI vs. Isotopic Resolution • Instrumental st = const (< 12 kDa) in time • Isotopic st ~ 2 time points (2-70 kDa)

  15. Effect of Resampling on TOF Signal • For all peaks • st = const(t) • Enhanced • sensitivity • for heavy ions

  16. Single Shot Noise Characteristics • 8-bit ADC • (max SNR = 30) • 2-point clock • feed in FFT • (high power) • 2-channel • differential • amplifier • (colored noise)

  17. Average Noise and Resampling • Gaussian noise • variance is • increased • 200-shot average • variance is • preserved

  18. Broad Range Deconvolution MH++SA -H2O +Na ApoAI+ H+ +SA +2SA

  19. Conclusions • Know hardware to design data processing - Baseline models - Dejittering and alignment - Resampling and deconvolution • Report uncertainties for data matrix • Comprehensive data analysis with VIBE-MS

  20. Acknowledgements $ Coming soon • H. Chen: Peak Detection (Wed.-11:45, #94 “State..” ) • VIBE-MS Workshop (dimaly@wm.edu) This work was supported by Virginia’s Commonwealth Research Technology Fund #IN2003-04, and Phase II SBIR grant from the National Cancer Institute CA101479 We thank our collaborators and coauthors from EVMS, W&M and INCOGEN for assistance with acquisition and analysis of calibration data for SELDI PBSII instrument We are grateful to Dr. Stacy Moore and Dr. Scott Weinberger from Ciphergen, Inc. for their help in clarifying instrumental specifications and parameters

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