pRolocmarkers: Organelle markers

In lgatto/pRoloc: A unifying bioinformatics framework for spatial proteomics

Organelle markers

Description

This function retrieves a list of organelle markers or, if no species is provided, prints a description of available marker sets. The markers can be added to and MSnSet using the addMarkers function. Several marker version are provided (see Details for additional information).

Usage

pRolocmarkers(species, version = "2")

Arguments

species	character(1) defining the species of interest. For reference species markers, this is just the species e.g. "hsap". For published marker sets this is the species and author name e.g. "hsap_geladaki".
version	character(1) defining the marker version. Default is "2".

Details

Version 1 of the markers have been contributed by various members of the Cambridge Centre for Proteomics, in particular Dr Dan Nightingale for yeast, Dr Andy Christoforou and Dr Claire Mulvey for human, Dr Arnoud Groen for Arabodopsis and Dr Claire Mulvey for mouse. In addition, original (curated) markers from the pRolocdata datasets have been extracted (see pRolocdata for details and references). Curation involved verification of publicly available subcellular localisation annotation based on the curators knowledge of the organelles/proteins considered and tracing the original statement in the literature.

Version 2 of the markers (current default) have been updated by Charlotte Hutchings from the Cambridge Centre for Proteomics. Reference species marker sets are the same as those in version 1 with minor corrections and an updated naming system. Version 2 also contains additional marker sets from spatial proteomics publications. References for the source publications are provided below:

• Geladaki, A., Britovsek, N.K., Breckels, L.M., Smith, T.S., Vennard, O.L., Mulvey, C.M., Crook, O.M., Gatto, L. and Lilley, K.S. (2019) Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics. Nature Communications. 10 (1). doi:10.1038/s41467-018-08191-w

• Christopher, J.A., Breckels, L.M., Crook, O.M., Vazquez–Chantada, M., Barratt, D. and Lilley, K.S. (2024) Global proteomics indicates subcellular-specific anti-ferroptotic responses to ionizing radiation.p.2024.09.12.611851. doi:10.1101/2024.09.12.611851

• Itzhak, D.N., Tyanova, S., Cox, J. and Borner, G.H. (2016) Global, quantitative and dynamic mapping of protein subcellular localization. eLife. 5. doi:10.7554/elife.16950

• Villanueva, E., Smith, T., Pizzinga, M., Elzek, M., Queiroz, R.M.L., Harvey, R.F., Breckels, L.M., Crook, O.M., Monti, M., Dezi, V., Willis, A.E. and Lilley, K.S. (2023) System-wide analysis of RNA and protein subcellular localization dynamics. Nature Methods. 1-12. doi:10.1038/s41592-023-02101-9

• Christoforou, A., Mulvey, C.M., Breckels, L.M., Geladaki, A., Hurrell, T., Hayward, P.C., Naake, T., Gatto, L., Viner, R., Arias, A.M. and Lilley, K.S. (2016) A draft map of the mouse pluripotent stem cell spatial proteome. Nature Communications. 7 (1). doi:10.1038/ncomms9992

• Barylyuk, K., Koreny, L., Ke, H., Butterworth, S., Crook, O.M., Lassadi, I., Gupta, V., Tromer, E., Mourier, T., Stevens, T.J., Breckels, L.M., Pain, A., Lilley, K.S. and Waller, R.F. (2020) A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions. Cell Host and Microbe. 28 (5), 752-766.e9. doi:10.1016/j.chom.2020.09.011

• Moloney, N.M., Barylyuk, K., Tromer, E., Crook, O.M., Breckels, L.M., Lilley, K.S., Waller, R.F. and MacGregor, P. (2023) Mapping diversity in African trypanosomes using high resolution spatial proteomics. Nature Communications. 14 (1), 4401. doi:10.1038/s41467-023-40125-z

Note: These markers are provided as a starting point to generate reliable sets of organelle markers but still need to be verified against any new data in the light of the quantitative data and the study conditions.

Value

Prints a description of the available marker lists if species is missing or a named character with organelle markers.

Author(s)

Laurent Gatto

See Also

addMarkers to add markers to an MSnSet and markers for more information about marker encoding.

Examples

pRolocmarkers()
pRolocmarkers("hsap")
table(pRolocmarkers("hsap"))

## Old markers
pRolocmarkers("hsap", version = "2")["Q9BPW9"]
pRolocmarkers("hsap", version = "1")["Q9BPW9"]

lgatto/pRoloc documentation built on Oct. 23, 2024, 12:51 a.m.