zMAP toolset: model-based analysis of large-scale proteomic data via a variance stabilizing z-transformation

被引：0

作者：

Gui, Xiuqi ^{[1
]}

Huang, Jing ^{[1
]}

Ruan, Linjie ^{[2
]}

Wu, Yanjun ^{[3
]}

Guo, Xuan ^{[1
]}

Cao, Ruifang ^{[1
]}

Zhou, Shuhan ^{[1
]}

Tan, Fengxiang ^{[1
]}

Zhu, Hongwen ^{[4
]}

Li, Mushan ^{[5
]}

Zhang, Guoqing ^{[1
]}

Zhou, Hu ^{[4
]}

Zhan, Lixing ^{[3
]}

Liu, Xin ^{[2
]}

Tu, Shiqi ^{[1
]}

Shao, Zhen ^{[1
]}

机构：

[1] Chinese Acad Sci, Univ Chinese Acad Sci, Shanghai Inst Nutr & Hlth, CAS Key Lab Computat Biol, Shanghai 200031, Peoples R China

[2] Chinese Acad Sci, Univ Chinese Acad Sci, Key Lab Epigenet Regulat & Intervent, Shanghai Inst Biochem Cell & Biol,CAS Ctr Excellen, Shanghai 200031, Peoples R China

[3] Chinese Acad Sci, Univ Chinese Acad Sci, Shanghai Inst Nutr & Hlth, CAS Key Lab Nutr Metab & Food Safety, Shanghai 200031, Peoples R China

[4] Chinese Acad Sci, Shanghai Inst Mat Med, Analyt Res Ctr Organ & Biol Mol, State Key Lab Drug Res, Shanghai 201203, Peoples R China

[5] Penn State Univ, Dept Stat, University Pk, PA 16802 USA

来源：

GENOME BIOLOGY | 2024年 / 25卷 / 01期

基金：

中国国家自然科学基金;

关键词：

INTEGRATED PROTEOGENOMIC CHARACTERIZATION; RELATIVE QUANTIFICATION; MOLECULAR SIGNATURES; RATIO COMPRESSION; METABOLISM; CANCER; ITRAQ; QUANTITATION; INSIGHTS; REVEALS;

D O I：

10.1186/s13059-024-03382-9

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Isobaric labeling-based mass spectrometry (ILMS) has been widely used to quantify, on a proteome-wide scale, the relative protein abundance in different biological conditions. However, large-scale ILMS data sets typically involve multiple runs of mass spectrometry, bringing great computational difficulty to the integration of ILMS samples. We present zMAP, a toolset that makes ILMS intensities comparable across mass spectrometry runs by modeling the associated mean-variance dependence and accordingly applying a variance stabilizing z-transformation. The practical utility of zMAP is demonstrated in several case studies involving the dynamics of cell differentiation and the heterogeneity across cancer patients.

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页数：30

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