As my understanding the package pRoloc allows one to study the localisation of protein inside cells , using relative quantitation of known organelle residents, termed organelle markers.
In the the vignette it uses `tan2009r1` data of markers that have been obtained by mining the pRolocdata datasets and curation by various members of the Cambridge Centre for Proteomics.
## ## Cytoskeleton ER Golgi Lysosome Nucleus ## 7 24 7 8 21 ## PM Peroxisome Proteasome Ribosome 40S Ribosome 60S ## 25 4 14 22 32 ## mitochondrion ## 15
This shows only markers for a subset of organelles: Cytoskeleton, ER, Golgi, Lysosome, Nucleus, PM (Plasma Membrane I assume), Peroxisome, ?Proteasome? (not sure what this is?), Ribosome 40S, Ribsome 60S, and Mitochondrion. It misses many other sub-cellular compartments like Cytosol, Actin Filaments, Vesicles, etc.
Are these markers for proteins that are only specific to the organelle of interest? Meaning, it is not a protein that can be found in other subcellular compartments (multi-localizing protein)
What I would like to do is use information from the Human Proteome Atlas with pRoloc's `addMarkers()` function. This way instead of 11 organelles I have data on more subcellular compartments. The subcellular location data from their website has many proteins which mult-localize. Can this data be used instead as marker data? Or can you only use pRolocmarkers (Homo sapiens only has 872 fir example) with their Uniprot Protein Identifiers