Table 2 |.
Recommended resources for subcellular proteomics data
| Data resource | Description | URL |
|---|---|---|
| Mass spectrometry-based proteomics | ||
| PRoteomics IDEntifications Database (PRIDE)307 | World’s largest data repository for a diverse range of MS workflows Mandatory submission requirements for each experiment include raw MS files and processed results showing protein identification Part of the ProteomeXchange Consortium |
https://www.ebi.ac.uk/pride |
| PeptideAtlas308 | A resource that provides both a uniform analysis pipeline and repository for genome annotation of raw tandem MS data | http://www.peptideatlas.org |
| Mass Spectrometry Interactive Virtual Environment (MassIVE)309 | Part of the ProteomeXchange Consortium A resource to allow the free exchange of MS data Includes proximity-dependent biotinylation data sets |
https://massive.ucsd.edu/ |
| Bespoke subcellular MS repositories and pipelines | ||
| ProHits-web | Repository for storing, visualizing and disseminating affinity purification MS and proximity labelling data Designed to complement MassIVE, BioGRID and IntAct, which also store interaction data |
https://prohits-web.lunenfeld.ca/ |
| The Cell Map160 | A large-scale project aiming to map the entire interaction network of the human embryonic kidney cell line, HEK293, as an open-access resource | https://humancellmap.org/ |
| pRoloc and pRolocdata253 | A series of R packages with user-friendly pipelines for data analysis of biochemical fractionation experiments The pRolocdata package contains existing spatial proteomics data sets from LOPIT and protein correlation profiling |
https://lgatto.github.io/pRoloc/ |
| SubCellBarCode47 | Exploratory web interface for localization data across five different human cancer cell lines collected from biochemical fractionation experiments | https://www.subcellbarcode.org/ |
| HeLa Spatial Proteome database44 | Interactive subcellular biochemical fractionation maps of the human cervical cancer cell line, HeLa | www.mapofthecell.org |
| MitoCarta310 | An inventory of highly confident human and mouse mitochondrial proteins annotated using multiple microscopy and genome-scale data sets | https://www.broadinstitute.org/mitocarta/ |
| MitoMiner | A database of mitochondrial localization experiments in mammals, zebrafish and yeasts | https://mitominer.mrc-mbu.cam.ac.uk/ |
| PeroxisomeDB311 | A curated resource collating identified peroxisomal proteins from 38 organisms | http://www.peroxisomedb.org/ |
| RareLSD312 | A manually curated inventory of lysosomal enzymes | https://webs.iiitd.edu.in/raghava/rarelsd/ |
| Imaging resources | ||
| Cell Image Library (CIL)313 | A public repository providing a resource of thousands of imaging data sets, including videos and animations, from various organisms | http://www.cellimagelibrary.org |
| Image Data Resource (IDR)314 | Publicly accessible light microscopy data alongside extensive metadata for the purpose of improving accessibility and reanalysis | https://idr.openmicroscopy.org |
| BioImage Archive | A central archive for data from the IDR and the Electron Microscopy Public Image Archive (EMPIAR) | https://www.ebi.ac.uk/bioimage-archive/ |
| Multidisciplinary repositories | ||
| Human Protein Atlas (HPA)11 | A large-scale project with open-source data that aims to map all human proteins in cells, tissues and organs, including subcellular information Data types include antibody-based imaging and systems biology data |
https://www.proteinatlas.org/ |
| Universal Protein Resource (UniProt)144 | A consortium of multiple databases providing protein sequence and annotation data Annotations are performed through automated and manual curation of information extracted from the literature and computational analyses such as Gene Ontology |
https://www.uniprot.org/ |
LOPIT, localization of organelle proteins using isotope tagging; MS, mass spectrometry.