Source: Proteomics, 2003, vol.3, pp.392-401 Authors: Paul Cutler, Geoffrey Heald, Ian R.

A novel approach to spot detection for two-dimensional gel electrophoresis images using pixel value collection Source: Proteomics, 2003, vol.3, pp.392-401 Authors: Paul Cutler, Geoffrey Heald, Ian R. White and Jason Ruan Speaker: Shu-Fen Chiou (邱淑芬) Date: 2005/03/18

Outline • Introduction • Proposed Method • Experimental results • Conclusions • Comment

Introduction • A common goal of proteomic analysis: Quantitation and identification of proteins which are differentially expressed under defined physiological conditions. • 2D-gel is a proteomic technology.

Introduction • Drawbacks of the available methods: • Noise and artefacts • Need extensive parameter setting • Take much time • Operator subjectivity • A new method using a segmentation method involving pixel value collection via serial analysis of the image through its range of density levels.

1616 2d gel image Proposed method • Smallest pixel value:246 • Highest pixel value:56 • Limits: • Size (maxSize, minSize) • Shape (ellipse or circle)

Proposed method High The first range:56~76 Threshold 1: (56+61+67)/3=61 56 61 67 The second range:105~125 Threshold 2: (105+109)/2=107 Range:20 105 109 Low

Proposed method Threshold 1:61 Find the pixel <= threshold 1 minSize:12 maxSize:28 Spot 1: (10,9), (10,10), (11,10)

Proposed method Threshold 2:107 Find the pixel <= threshold 2 minSize:12 maxSize:28 Spot 1: (10,9), (10,10), (11,10), (9,9), …

Experimental results

Compare with edge detection Edge detection Proposed method

Conclusions • The method can be automated and hence reduce operator subjectivity. • The method can detect a large dynamic range of spot intensities and areas, and has the potential to detect and resolve merged spots.

Comment Find the spots using the pixel value collection

Source: Proteomics, 2003, vol.3, pp.392-401 Authors: Paul Cutler, Geoffrey Heald, Ian R.