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. 2024 Jan 5;52(D1):D562-D571.
doi: 10.1093/nar/gkad1018.

SPDB: a comprehensive resource and knowledgebase for proteomic data at the single-cell resolution

Fang Wang  1   2 , Chunpu Liu  1 , Jiawei Li  3 , Fan Yang  2 , Jiangning Song  4 , Tianyi Zang  1 , Jianhua Yao  2 , Guohua Wang  1
Affiliations

SPDB: a comprehensive resource and knowledgebase for proteomic data at the single-cell resolution

Fang Wang et al. Nucleic Acids Res. .

Abstract

The single-cell proteomics enables the direct quantification of protein abundance at the single-cell resolution, providing valuable insights into cellular phenotypes beyond what can be inferred from transcriptome analysis alone. However, insufficient large-scale integrated databases hinder researchers from accessing and exploring single-cell proteomics, impeding the advancement of this field. To fill this deficiency, we present a comprehensive database, namely Single-cell Proteomic DataBase (SPDB, https://scproteomicsdb.com/), for general single-cell proteomic data, including antibody-based or mass spectrometry-based single-cell proteomics. Equipped with standardized data process and a user-friendly web interface, SPDB provides unified data formats for convenient interaction with downstream analysis, and offers not only dataset-level but also protein-level data search and exploration capabilities. To enable detailed exhibition of single-cell proteomic data, SPDB also provides a module for visualizing data from the perspectives of cell metadata or protein features. The current version of SPDB encompasses 133 antibody-based single-cell proteomic datasets involving more than 300 million cells and over 800 marker/surface proteins, and 10 mass spectrometry-based single-cell proteomic datasets involving more than 4000 cells and over 7000 proteins. Overall, SPDB is envisioned to be explored as a useful resource that will facilitate the wider research communities by providing detailed insights into proteomics from the single-cell perspective.

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Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
Demonstration of data search and exploration in SPDB. (A) The browse interface and filter components of all collected datasets in SPDB. (B) The data information panel of SPDB. (C) The UMAP visualization panel of SPDB. (D) The protein comparison panel of SPDB. (E) The analysis result panel of SPDB.
Figure 2.
Figure 2.
Demonstration of protein search and exploration in SPDB. (A) The protein search page of SPDB. (B) An example of available protein list resulting from fuzzy search. (C) The table of protein candidates detected in at least one dataset. (D) The protein summary panel of SPDB. (E) The browse interface of the related datasets and new pop-up window for one selected dataset.
Figure 3.
Figure 3.
Demonstration of data comparison in SPDB. (A) The browse interface of the related datasets. (B) The comparison of protein expressions under two selected datasets. (C) The comparison of protein correlation patterns under two selected datasets.
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