Any Resource For Relative Protein Abundances By Cell Or Organelle?

Question

[Alastair Kerr]

I am looking to determine whether the proteins I find from a proteomics experiment have been found because they are simply the most common in that cell type (or organelle) or are a consequence of some other factor.

Does anyone know if such a resource of relative protein abundances exists? I've looked at the Human Protein Atlas and the Human Protein Reference Database and cannot find this type of information. Am I missing something or are there any relevant resources?

[Casey Bergman]

Are you interested in human data or protein abundance data in general?

[Alastair Kerr]

Human just now, but it is a technique I'd like to add to my repetoire

Answer 1

[Lyco]

You should have a look at pax-db, which collects abundance information for 10 species (including human, yeast, fly, arabidopsis). As far as I know the database collects this information from various proteomics experiments and offers some kind of 'consensus abundance' per organism. If you really need this information for a particular cell type, there is probably no other choice than looking for individual proteomics projects.

Answer 2

[Casey Bergman]

For yeast, protein abundances have been measured systematically across the genome by Ghaemmaghami et al (2003). The data can be queried at the Yeast GFP Fusion Localization Database.

Answer 3

[Khader Shameer]

I think you can perform an enrichment analysis to assess relative abundance using Cellular Component category in Gene-Ontology.

Other option is to use statistical test to assess the sub-cellular localization of your protein of interest with respect to human proteome. You can download sub-cellular localization from Uniprot for human proteome. Please see this detailed post for a detailed account of GO enrichment analysis.

EDIT: this method may not be appropriate if you are looking for a quantitative approach based on the "protein abundance".

[Alastair Kerr]

Thanks but it is tne abundance, (comparitive protein concentrations), I am interested in.

[Khader Shameer]

Yeah. The approach I mentioned is useful to get a count, not the abundance in ppm.

Answer 4

[unksci]

It is the year 2016, and I have a question, which is highly similar to the one, which has been posted 5 years ago:

Is there any resource, with a deep coverage that lists abundance in nuclear and cytoplasmic fraction of a human cell line or tissue?