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QA/QC of SELDI Data in Clinical Studies. 6-8-2006 CAMDA. Simon Lin Northwestern University. CDC Toni Whistler Suzanne Vernon Northwestern Pan Du Warren Kibbe Simon Lin. Duke Radiology Ned Patz Mike Campa Duke Bioinformatics Patrick McConnell Rich Haney Sal Mungal.

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Qa qc of seldi data in clinical studies l.jpg

QA/QC of SELDI Data in Clinical Studies

6-8-2006 CAMDA

Simon Lin

Northwestern University


Acknowledgements l.jpg

CDC

Toni Whistler

Suzanne Vernon

Northwestern

Pan Du

Warren Kibbe

Simon Lin

Duke Radiology

Ned Patz

Mike Campa

Duke Bioinformatics

Patrick McConnell

Rich Haney

Sal Mungal

Acknowledgements


Agenda l.jpg
Agenda

  • Challenges in clinical proteomics

  • Hypothesis: QA/QC is the key

  • Potential biomarkers of CFS

  • Future: Online QC


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“The standard procedure of using SELDI-TOF mass spectra to construct a classifier is ________ . ”

- Dr. Brian Luke, NCI

“The proper construction of SELDI-TOF-based classifiers for early disease detection”, CHI Proteomics Conference Brochure, 2006

WRONG


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TEMPERAMENTAL construct a classifier is ________ . ”

“Mass spectrometers can be __________. ”

- Coombes et. al., Nature Biotechnology, 3: 291-292, 2005


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Evidences (I) construct a classifier is ________ . ”

Gusev et. al., Analytical Chemistry 67: 1034, 1995


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Evidences (II) construct a classifier is ________ . ”

- Image from Invitrogen.co.jp


Evidences iii l.jpg
Evidences (III) construct a classifier is ________ . ”

  • Same biological sample

  • Technical Replicates

  • m/z: 5.0K to 8.5K

  • CAMDA’06 QC serum


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Hypothesis construct a classifier is ________ . ”

Removing spectra of poor quality will improve our capability to detect biomarkers.


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How to measure quality construct a classifier is ________ . ”

  • Classification confidence

  • Correlation coefficient: r2

  • Principal component analysis

  • Signal-to-noise Ratio (SNR)

  • After-the-fact: QA

  • On-the-spot: QC


Why wavelet l.jpg
Why Wavelet construct a classifier is ________ . ”

  • Can be directly applied to raw data

  • Mutliscale analysis

    • Noise

    • Signal

    • Baseline


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Wavelets construct a classifier is ________ . ”

  • A data projection method

    • From raw data space to wavelet space

    • c.f. Fourier transform

  • A multi-resolution analysis method

    • Finer v.s. coarse scale


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Estimating SNR construct a classifier is ________ . ”

  • Global method

    • Partition the measurements into noise, signal, and baseline

  • Local method

    • For each peak, estimate the SNR

Raw data

Signal

Noise


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Raw spectrum construct a classifier is ________ . ”

QA step

DWT-based SNR estimation

Baseline removal and

normalization

Spectrum alignment

CWT-based peak detection

Classification and other

data analysis

Biomarker identification

by statistical tests


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Improved biomarker detection construct a classifier is ________ . ”

QA cutoff: SNR > 5


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Advantages of SNR construct a classifier is ________ . ”

  • Complementary to outlier-resistant statistics

  • Online QC

    • Simple

    • Can be done in real time


Conclusions l.jpg
Conclusions construct a classifier is ________ . ”

“Mass spectrometers can be __________. ”

ONLINEQUALITY CONTROL

- Coombes et. al., Nature Biotechnology, 3: 291-292, 2005

TEMPERAMENTAL

“_________ nature of conclusions of most serum proteomics studies.”

PROVISIONAL


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Ben Bolstad, PLM Image Hall of Fame construct a classifier is ________ . ”

http://plmimagegallery.bmbolstad.com


Must read papers l.jpg
Must read papers construct a classifier is ________ . ”

  • The Ovarian cancer controversy

  • Wavelet smoothing


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Proteomics Challenges construct a classifier is ________ . ”

Hilario et al., Mass Spectrometry Reviews, 25: 409-449, 2006