1.1. Search for single-cell proteomic data

At the top of the home page in SingPro, there is a quick search box where users can search datasets by enter desired features of the data, including project ID, diseases, cell lines, tissue, quantitative methods, etc. In addition to the quick search, a drop-down search box is also provided, users can explore flow cytometry-based (FC-SCP) or mass spectrometry-based data (MS-SCP) separately by selecting Tissue/Organ, Cell Type, Disease Class, Experiment Method, Quantification Strategy in the corresponding drop-down menu.

1.2. Result of data search

For search result, take searching “Acute myeloid leukemia” as example, studies that match the searched condition are displayed on the results interface, where flow cytometry-base and mass spectrometry- based studies were displayed in different color (orange for FC-SCP, blue for MS-SCP), basic information such as Tittle, Species, Tissue, Condition, Methods, and Description of the study were also provided to facilitated data selection. User can see detailed description of the study by clicking the “Project Detail”.

2.1. Description of flow cytometry-based single-cell proteomics

2.1.1. General information for FC-SCP

For each FC-SCP, “SCP52724” as example, general information of the dataset is described in the upper section of the webpage which includes: Project ID, Project Title, Description, Research Type, Publication linkage to the original article, brief introduction and linkage to three well established Data Processing & Analysis Tools (Anpela, Cytobank and FlowJo).

2.1.2. Description of biological samples and experimental procedure for FC-SCP

The following is a detailed description of the experimental process. A typical SingPro page describing the quantification process for flow cytometry-based SCP. Each page is carefully organized into three sections: Biological Information (studied species, experiment tissue/organ, analyzed cell type, pathological/physiological conditions, etc.), Single-cell Proteomic Quantification (applied quantification approach, experimental platform, methods for data processing and analysis, etc.), and Protein Panel (fluorochrome, protein marker, external link, clone, category (surface/intracellular) and panel number).

2.1.3. Protein expression differences of FC-based SCP

A typical SingPro page describing the expression variations of studied protein among multiple groups using flow cytometry-based SCP data. All proteins in staining panel are included into the drop-down-box where a user can select the protein of interest. The p-value of the selected protein between two groups is calculated and provided.

2.2. Description of mass spectrometry -based single-cell proteomics

2.2.1. General information for MS-SCP

For each MS-SCP, “SCP52016” as example, general information of the dataset is described in the upper section of the webpage which includes: Project ID, Project Title, Description, Research Type, Sample Type and Publication linkage to the original article.

2.2.2. Description of biological samples and experimental procedure for MS-SCP

The following is a detailed description of the experimental process. A typical SingPro page describing quantification process for mass spectrometry-based SCP. Each page is carefully organized to four sections: Studied Single-cell Type (studied species, cells, pathological/physiological condition, etc.), Sorting Method (method name & its application detail), Preparation Method (method name & its application detail), and Quantification Process (applied quantification approach, quantificiation strategy, experimental platform, etc.).

2.2.3. Protein expression differences of MS-based SCP

A typical SingPro page describing the expression variations of studied protein among multiple groups using mass spectrometry-based SCP data. Particularly, the volcanic map between two groups is calculated to provide the differential expression profiles for proteins (the horizontal coordinate indicates the log2 fold change (Log2FC) and vertical one denotes log p-value (LogP); the proteins are colored in red and blue based on their Log2FC & p-value (Log2FC >1 & p-value <0.05 and Log2FC <-1 & p-value <0.05, respectively). The differentially expressed proteins can be selected, and the p-value of selected protein between two groups is calculated and provided.

For FC- SCP data, SingPro provides the raw data (in fcs format) and corresponding metadata, and provides a Download ID for each file, and describes the corresponding protein detection panel. For MS- SCP data, SingPro provides the raw data and corresponding processed files including metadata, FASTA and PEAK data files, and provides a Download ID for each file. Users can download each data by clicking the Download Button, or use the batch download tool provided in the website, can click to view the detailed tutorial of the batch download tool.

Any benefit from the use of the data therein shall be vested in the original author of the dataset.