About the T-Cell Subcellular Atlas

This app is intended as interactive supplement to the publication:

TcellSubC: An Atlas of the Subcellular Proteome of Human T Cells


Rubin Narayan Joshi, Charlotte Stadler, Robert Lehmann, Janne Lehtiö, Jesper Tegnér, Angelika Schmidt, and Mattias Vesterlund
frontiers in Immunology
https://doi.org/10.3389/fimmu.2019.02708

Explore the subcellular localization of proteins human T cells


We have curated a high resolution subcellular proteomic map of primary human T cells, divided into cytosolic, nuclear and membrane (including organelles) fractions under steady state conditions and upon 15 minutes and 1 hour of T cell receptor (TCR) stimulation respectively. We quantified the subcellular distribution of 7122 proteins and identified a subset of 210 potentially translocating proteins, including both well-known examples and novel ones. Microscopic validation confirmed the localization of selected proteins with previously known and unknown localization respectively.

Experimental Outline

CD4+ T cells from 3 donors were stimulated for 15 min or 1 h with cross linked anti-CD3/anti-CD28 antibodies (TCR stimulation) or processed as untreated. The cells upon fractionation were analyzed in MS as represented in the workflow. The subcellular fractions and time points of activation are represented by individual colors.

Western Blot evaluation of subcellular fractionation

A representative immunoblot of the 3 subcellular components after fractionation probed with antibodies against markers of specific subcellular location as represented.

PCA all fractions and donors

Principle Component Analysis was performed on the TMT intensity ratios of individual components and timepoints from each donor normalized to the internal standard. The fractions are represented by individual colors and the donors are represented by individual shapes.

Heat map all fractions and donors

The heat map depicts log2 values of TMT intensity ratios and represented according to the indicated row normalized color scheme. The columns are clustered by average linkage method using 1 minus Pearson correlation. The rows are clustered by k means clustering (k=3) by 1 minus Pearson correlation. The clusters are represented in individual colors.

Protein Abundance Profile



Plot the abundance for an individual protein, separately for the three compartments. Different donors are shown in red, green, and blue dots while the average is shown as black line.

1. To display a specific protein, enter the protein symbol in the search field below.
2. The detailed information is displayed when hovering the cursor over the dot in the plot.
3. To hide a specific donor, click on the corresponding dot in the legend.
4. A table with UniProt IDs and Gene Ontology terms for the selected protein is shown below the plot.

TCR Stimuation (Minutes)

Mean Protein Abundance per Treatment



Examine the abundance distribution over all proteins in a specific treatment (0/15/60 min TCR stimulation)

Protein Fold-Changes in Different Compartments



Which proteins change in abundance in response to TCR stimulation?

Paired analyses of the MS data were conducted using Limma and the DeqMS R-package. The overlapping proteins from the 3 sets (donors), with full quantitation in all channels was imported into and used as a matrix. The PSM count table was generated by taking the median number of PSMs used for identification across the 3 TMT-sets. Paired analysis was carried out (within donor as a pair) and the three different time points (resting, 15 and 60 min) within each fraction being compared.