Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project

Marcin Adamski, Thomas Blackwell, Rajasree Menon, Lennart Martens, Henning Hermjakob, Chris Taylor, Gilbert S. Omenn and David J. States

2.1 Introduction 37

2.2 Materials and methods 39

2.2.1 Development of the data model 39

2.2.1.1 Laboratory 39

2.2.1.2 Experimental protocol 39

2.2.1.3 Protein identification data set 39

2.2.1.4 Peak list 41

2.2.1.5 Summary of technologies and resources 41

2.2.1.6 MS/MS spectra 41

2.2.1.7 SELDI peak list 42

2.2.2 Data submission process 42

2.2.3 Design ofthe data repository 42

2.2.4 Receipt of the data 43

2.3 Inference from peptide level to protein level 44

2.4 Summary of contributed data 46

2.4.1 Cross-laboratory comparison, confidence of the identifications 49

2.5 False-positive identifications 51

2.6 Data dissemination 56

2.7 Discussion 57

2.8 Concluding remarks 58

2.9 Computer technologies applied 60

2.10 References 61

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