HUPO Plasma Proteome Project specimen collection and handling Towards the standardization of parameters for plasma proteome samples

Alex J. Rai, Craig A. Gelfand, Bruce C. Haywood, David J. Warunek, Jizu Yi, Mark D. Schuchard, Richard J. Mehigh, Steven L. Cockrill, Graham B. I. Scott, Harald Tammen, Peter Schulz-Knappe, David W. Speicher, Frank Vitzthum, Brian B. Haab, Gerard Siest and Daniel W. Chan

3.1 Introduction 63

3.2 Materials and methods 65

3.2.1 HUPO reference sample collection protocol 65

3.2.2 Differential peptide display 66

3.2.3 Stability studies and SELDI analysis 66

3.2.4 SDS-PAGE analysis for stability studies 67

3.2.5 2-DE for stability studies 67

3.2.6 SELDI-TOF analysis for protease inhibitor studies 67

3.2.7 2-DE for plasma protease inhibition studies 68

3.2.8 Tryptic digestion and protein identification for protease inhibition studies 69

3.2.9 Antibody microarray analysis using two-color rolling circle amplification 69

3.3 Results 69

3.3.1 Comparisons of specimen types 73

3.3.1.1 Analysis of serum 73

3.3.1.2 Analysis of plasma 73

3.3.2 Evaluation of storage and handling conditions 73

3.3.3 Evaluations of the use of protease inhibitors 73

3.3.3.1 Analysis with SELDI-TOF MS of "time zero" effects of protease inhibitors in plasma 73

3.3.3.2 Analysis by 2-DE 73

3.3.3.3 Analysis with antibody arrays 76

3.4 Discussion 77

3.4.1 Other pre-analytical variables and control considerations 83

3.4.2 Reference materials 84

3.5 Concluding remarks 87

3.6 References 88

Was this article helpful?

0 0

Post a comment