Standardizing Proteomics Workflow for Liquid Chromatography-Mass Spectrometry: Technical and Statistical Considerations

Journal of Proteomics & Bioinformatics
Sudhir SrivastavaShesh N Rai

Abstract

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. 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. We found that the FFPE TSM is better than the FR TSM. We also found that the one-step 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.

Citations

Aug 25, 2020·Medicinal Chemistry Research : an International Journal for Rapid Communications on Design and Mechanisms of Action of Biologically Active Agents·Jian JinRussell A Prough
Jun 21, 2020·Journal of the American Society of Nephrology : JASN·Michael L MerchantKenneth R McLeish
Mar 5, 2021·Journal of Proteome Research·David MorgensternYishai Levin

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Methods Mentioned

BETA
laser capture microdissection

Software Mentioned

Mascot
R vsn
R package “ imputeLCMD ”
MasslVE
R
R package “ preprocessCore ”
Sequest
TSM×TEM

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