Standardizing Proteomics Workflow for Liquid Chromatography-Mass Spectrometry: Technical and Statistical Considerations
Received Date: Mar 01, 2019 / Accepted Date: Mar 27, 2019 / Published Date: Apr 04, 2019
Introduction: The quantitative measurements based on liquid chromatography (LC) coupled with mass spectrometry (MS) often suffer from the problem of missing values and data heterogeneity from technical variability. We considered a proteomics data set generated from human kidney biopsy material to investigate the technical effects of sample preparation and the quantitative MS.
Methods: We studied the effect of tissue storage methods (TSMs) and tissue extraction methods (TEMs) on data analysis. There are two TSMs: frozen (FR) and FFPE (formalin-fixed paraffin embedded); and three TEMs: MAX, TX followed by MAX and SDS followed by MAX. We assessed the impact of different strategies to analyze the data while considering heterogeneity and MVs. We have used analysis of variance (ANOVA) model to study the effects due to various sources of variability.
Results and Conclusion: We found that the FFPE TSM is better than the FR TSM. We also found that the onestep TEM (MAX) is better than those of two-steps TEMs. Furthermore, we found the imputation method is a better approach than excluding the proteins with MVs or using unbalanced design.
Keywords: ANOVA; Imputation; Proteins; Tissue storage; Tissue extraction; Technical variability
Citation: Srivastava S, Merchant M, Rai A, Rai SN (2019) Standardizing Proteomics Workflow for Liquid Chromatography-Mass Spectrometry: Technical and Statistical Considerations. J Proteomics Bioinform 12: 048-055. Doi: 10.4172/0974-276X.1000496
Copyright: © 2019 Srivastava S, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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