Question: Any Resource For Relative Protein Abundances By Cell Or Organelle?
10
gravatar for Alastair Kerr
8.2 years ago by
Alastair Kerr5.2k
The University of Edinburgh, UK
Alastair Kerr5.2k wrote:

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?

protein • 3.6k views
ADD COMMENTlink modified 3.1 years ago by unksci150 • written 8.2 years ago by Alastair Kerr5.2k

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

ADD REPLYlink written 8.2 years ago by Casey Bergman18k

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

ADD REPLYlink written 8.2 years ago by Alastair Kerr5.2k
6
gravatar for Lyco
8.2 years ago by
Lyco2.3k
Germany
Lyco2.3k wrote:

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.

ADD COMMENTlink written 8.2 years ago by Lyco2.3k
1
gravatar for Casey Bergman
8.2 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

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.

ADD COMMENTlink written 8.2 years ago by Casey Bergman18k
0
gravatar for Khader Shameer
8.2 years ago by
Manhattan, NY
Khader Shameer18k wrote:

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".

ADD COMMENTlink modified 8.2 years ago • written 8.2 years ago by Khader Shameer18k

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

ADD REPLYlink written 8.2 years ago by Alastair Kerr5.2k

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

ADD REPLYlink written 8.2 years ago by Khader Shameer18k
0
gravatar for unksci
3.1 years ago by
unksci150
unksci150 wrote:

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?

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by unksci150
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