zMAP toolset: model-based analysis of large-scale proteomic data via a variance stabilizing z-transformation
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.
Authors
- Mushan Li (ORCID: https://orcid.org/0000-0003-2727-950X)
- Shiqi Tu (ORCID: https://orcid.org/0000-0003-3534-5714)
- Xiuqi Gui (ORCID: https://orcid.org/0009-0002-7680-477X)
- Hongwen Zhu (ORCID: https://orcid.org/0000-0002-2116-4245)
- Lixing Zhan (ORCID: https://orcid.org/0000-0003-4949-4358)
- Fengxiang Tan
- Shuhan Zhou (ORCID: https://orcid.org/0000-0002-7131-5144)
- Li Ruan (ORCID: https://orcid.org/0000-0002-2386-961X)
- Hu Zhou (ORCID: https://orcid.org/0000-0001-7006-4737)
- Ruifang Cao
- Xin Liu (ORCID: https://orcid.org/0000-0003-3256-2940)
- Yanjun Wu (ORCID: https://orcid.org/0000-0003-0233-2917)
- Zhen Shao (ORCID: https://orcid.org/0000-0002-4934-4360)
- Xuan Guo (ORCID: https://orcid.org/0000-0001-8560-6076)
- Guoqing Zhang (ORCID: https://orcid.org/0000-0002-9008-9568)
- Jing Huang (ORCID: https://orcid.org/0000-0001-6181-7565)
Institutions
- Pennsylvania State University (US)
- Chinese Academy of Sciences (CN)
- Shanghai Institute of Nutrition and Health (CN)
- Shanghai Institute of Materia Medica (CN)
- Center for Excellence in Molecular Cell Science (CN)
- University of Chinese Academy of Sciences (CN)
Publication Details
- Journal
- Genome biology
- Published
- 2024-10-14
- DOI
- https://doi.org/10.1186/s13059-024-03382-9
- Citations
- 2
- Primary Topic
- Advanced Proteomics Techniques and Applications
- Type
- article
- Field-Weighted Citation Impact
- 0.48
Funders
- St. Jude Children's Research Hospital
- National Natural Science Foundation of China
- Chinese Academy of Sciences
- National Key Research and Development Program of China