MetaMSD: meta analysis for mass spectrometry data

PeerJ

article

So Young Ryu¹  George A. Wendt¹ 

[1] School of Community Health Sciences, University of Nevada - Reno;Department of Epidemiology, University of California

关键词: Mass Spectrometry;    Differential Proteins;    Proteomics;    Meta-Analysis;   

DOI  :  10.7717/peerj.6699

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Mass spectrometry-based proteomics facilitate disease understanding by providing protein abundance information about disease progression. For the same type of disease studies, multiple mass spectrometry datasets may be generated. Integrating multiple mass spectrometry datasets can provide valuable information that a single dataset analysis cannot provide. In this article, we introduce a meta-analysis software, MetaMSD (Meta Analysis for Mass Spectrometry Data) that is specifically designed for mass spectrometry data. Using Stouffer’s or Pearson’s test, MetaMSD detects significantly more differential proteins than the analysis based on the single best experiment. We demonstrate the performance of MetaMSD using simulated data, urinary proteomic data of kidney transplant patients, and breast cancer proteomic data. Noting the common practice of performing a pilot study prior to a main study, this software will help proteomics researchers fully utilize the benefit of multiple studies (or datasets), thus optimizing biomarker discovery. MetaMSD is a command line tool that automatically outputs various graphs and differential proteins with confidence scores. It is implemented in R and is freely available for public use at https://github.com/soyoungryu/MetaMSD. The user manual and data are available at the site. The user manual is written in such a way that scientists who are not familiar with R software can use MetaMSD.

【 授权许可】

CC BY