zMAP toolset: model-based analysis of large-scale proteomic data via a variance stabilizing z-transformation
2024
Xiuqi Gui | Jing Huang | Linjie Ruan | Yanjun Wu | Xuan Guo | Ruifang Cao | Shuhan Zhou | Fengxiang Tan | Hongwen Zhu | Mushan Li | Guoqing Zhang | Hu Zhou | Lixing Zhan | Xin Liu | Shiqi Tu | Zhen Shao
Abstract 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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