Informatics and statistics for analyzing 2-d gel electrophoresis images.
Despite recent progress in "shotgun" peptide separation by integrated liquid chromatography and mass spectrometry (LC/MS), proteome coverage and reproducibility are still limited with this approach and obtaining enough replicate runs for biomarker discovery is a challenge. For these reasons, recent research demonstrates that there is a continuing need for protein separation by two-dimensional gel electrophoresis (2-DE). However, with traditional 2-DE informatics, the digitized images are reduced to symbolic data through spot detection and quantification before proteins are compared for differential expression by spot matching. Recently, a more robust and automated paradigm has emerged where gels are directly aligned in the image domain before spots are detected across the whole image set as a whole. In this chapter, we describe the methodology for both approaches and discuss the pitfalls present when reasoning statistically about the differential protein expression discovered.
Dowsey
Andrew W
AW
Institute of Biomedical Engineering, Imperial College London, London, UK.
Morris
Jeffrey S
JS
Gutstein
Howard B
HB
Yang
Guang-Zhong
GZ
D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D048088:Informatics / Q000379:methods; D011506:Proteins / Q000032:analysis* / Q000378:metabolism; D020543:Proteome / Q000032:analysis / Q000378:metabolism; D012984:Software
D011506:Proteins; D020543:Proteome