Single-cell Proteomic DataBase (SPDB) is a comprehensive repository for general single-cell proteomic data, encompassing both antibody-based and mass spectrometry-based single-cell proteomics, and provides dataset/protein search, visualization and download with unified formats.

Manual

Browsing datasets
The Data page contains a list of all the datasets incorporated in SPDB. The important information of datasets such as Species, Tissues and Technology are visualized in columns and are searchable. Users can browse all the datasets within the list and search interested datasets with specific information.
(1) Select "Data" to enter this page.
(2) Search datasets by specific information.
(3) Choose one dataset of interest to explore.
Exploring data
The page of data exploration contains five modules to help users to explore data in detail.
(1) Show some important information of the dataset.
(2) Explore the cell metadata and protein level of the dataset by UMAP visualization.
(3) Show some analysis plots of the dataset.
(4) Explore the expression level of two proteins simultaneously.
(5) Download the preprocessed file in .rds format.
Visualizing data
The visualization module of data exploration page can give users intuitive understanding of the dataset. Users can select “Protein Name” or “Cell Metadata” to change colors of cells in the corresponding UMAP plot and update the statistic of cells' property in the right panel.
Gating protein
The protein gating module of data exploration page can give users comparative understanding of two different proteins’ level under different cell metadata. Users can select “X-Axis Protein”, “Y-Axis Protein” and “Target” to change the x/y-axis level and color of each cell in the scatter plot.
Searching proteins
The Protein page contains the search function of proteins contained in SPDB. Users can select or input the protein name/accession/gene name of an interested protein (for example CD4) and select the target species to search information of the protein.
(1) Select "Protein" to enter this page.
(2) Enter Protein Name/Accession Number/Gena Name to search available proteins.
(3) Choose one interested protein from the table of protein candidates to explore.
Exploring proteins
The page of protein exploration contains two modules to help users to explore proteins in detail.
(1) Show some summary information of the protein (from Uniprot database).
(2) List the corresponding datasets which detect the protein in single cell level. Users can browse and filter these datasets and chose one to explore.
Data comparison
The Datasets tab in the page of one searched protein provides two data comparison functions.
(1) Users can choose two interested proteins from the data list to compare.
(2) Choose "Compare Expression" to compare protein expression between two datasets.
(3) Choose "Compare Correlation" to compare protein correlation patters between two datasets.

SPDB is developed by Tencent AI Lab and Harbin Institute of Technology. For help, please refer to the Manual link in the navigation bar, or contact us via avonwanghit@gmail.com.