Table I. Global organelle profiling studies with large subcellular localization datasets (since 2016).
| Profiling method/Lab | Separation technique | Quantification strategy | Clustering method | Visualization | Cell type/tissue | Refs | Localization data available from |
|---|---|---|---|---|---|---|---|
| Protein Correlation Profiling (PCP) (Mann Lab) | Velocity gradient centrifugation | Label-free | HC, PCP, SVM | HC | Mouse liver | (18) | http://nafld-organellemap.org/ |
| HyperLOPIT (Lilley Lab) | Density gradient centrifugation | TMT | SVM | PCA | Mouse ES cells | (20) | http://spatialmap.org/ |
| SVM | PCA | U2OS (human) | (15) | Supplemental Data of Ref. | |||
| SVM | PCA, t-SNE | Arabdidopsis thaliana callus | (22) | Supplemental Data of Ref. | |||
| SVM | PCA | Saccharomyces cerevisiae | (24) | https://proteome.shinyapps.io/yeast2018/ | |||
| SVM | PCA | Cyanobacterium synechocystis | (23) | https://lgatto.shinyapps.io/synechocystis/ | |||
| LOPIT variant (Cristea Lab) | Density gradient centrifugation | TMT | RF, NN, SVM | t-SNE | Human fibroblasts | (25) | Supplemental Data of Ref. |
| Dynamic Organellar Maps (Borner Lab) | Differential centrifugation | SILAC | SVM | PCA | HeLa (human) | (12) | www.mapofthecell.org |
| Label-free; SILAC; TMT | SVM | PCA | Mouse primary neurons | (17) | Supplemental Data of Ref. | ||
| SILAC | SVM | PCA | MutuDC (mouse) | (26) | http://dc-biology.mrc-lmb.cam.ac.uk | ||
| LOPIT-DC (Lilley Lab) | Differential centrifugation | TMT | SVM | PCA | U2OS (human) | (27) | https://proteome.shinyapps.io/lopitdc-u2os2018/ |
| Prolocate (Lobel Lab) | Differential and density gradient centrifugation | iTRAQ, TMT | PCP | PCA | Rat liver | (19) | http://prolocate.cabm.rutgers.edu/index.cgi |
| SubCellBarCode (Lehtiö Lab) | Differential centrifugation and detergent extraction | TMT | SVM | t-SNE | A431, U251, MCF7, NCIH322, HCC827 (human) | (21) | https://www.subcellbarcode.org/ |
Other main resources for spatial proteomes are the imaging-based Human Cell Atlas (https://www.proteinatlas.org/humanproteome/cell), the first proximity labelling based organellar map (https://cell-map.org/), the UniProt database (https://www.uniprot.org), and the Compartments database (https://compartments.jensenlab.org/Search).
Abbreviations: HC, Hierarchical Clustering; NN, Neural Networks; PCA, Principal Component Analysis; PCP, Protein Correlation Profiling; RF, Random Forest; SVM, Support Vector Machine; t-SNE, t-distributed Stochastic Neighbor Embedding; UMAP, Uniform Manifold Approximation and Projection for Dimension Reduction.