Integrating Multiple Quantitative Proteomic Analyses Using MetaMSD

So Young Ryu; Miriam P Yun; Sujung Kim

doi:10.1007/978-1-0716-1967-4_16

Integrating Multiple Quantitative Proteomic Analyses Using MetaMSD

Methods Mol Biol. 2023:2426:361-374. doi: 10.1007/978-1-0716-1967-4_16.

Authors

So Young Ryu¹, Miriam P Yun², Sujung Kim³

Affiliations

¹ School of Public Health, University of Nevada Reno, Reno, NV, USA. soyoungr@unr.edu.
² Department of Psychology Institute for Neuroscience, University of Nevada Reno, Reno, NV, USA.
³ School of Public Health, University of Nevada Reno, Reno, NV, USA.

PMID: 36308697
DOI: 10.1007/978-1-0716-1967-4_16

Abstract

MetaMSD is a proteomic software that integrates multiple quantitative mass spectrometry data analysis results using statistical summary combination approaches. By utilizing this software, scientists can combine results from their pilot and main studies to maximize their biomarker discovery while effectively controlling false discovery rates. It also works for combining proteomic datasets generated by different labeling techniques and/or different types of mass spectrometry instruments. With these advantages, MetaMSD enables biological researchers to explore various proteomic datasets in public repositories to discover new biomarkers and generate interesting hypotheses for future studies. In this protocol, we provide a step-by-step procedure on how to install and perform a meta-analysis for quantitative proteomics using MetaMSD.

Keywords: Integrating multiple differential analyses; Mass spectrometry data analysis; Meta-analysis; Proteomic software; Quantitative proteomics.

Publication types

Meta-Analysis
Research Support, N.I.H., Extramural

MeSH terms

Biomarkers
Mass Spectrometry / methods
Proteomics* / methods
Software*

Substances

Biomarkers

Grants and funding

R15 GM126562/GM/NIGMS NIH HHS/United States