Where can I find the content value of proteins in different subcellular localization

Question

[xidianbill]

Hi, guys. I want to know the specific content of proteins in different subcellular localization. Does anybody know where I can find this kind of data? And I wonder if there is some high-throughout way to measure the protein content.

[natasha.sernova]

See these posts from biostars:

Protein Subcellular Localization Prediction

Subcellular Localization

subcellular localization human / Mouse / Rat

what is the Query to find proteins which Subcellular location have Manually-assigned evidence in uniprot ?

See also the following paper and its chapter 3.5 (Comparison with high-throughput experimental data):

BaCelLo: a balanced subcellular localization predictor Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli and Rita Casadio
Biocomputing Group, Dept. of Biology University of Bologna

https://watermark.silverchair.com/btl222.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAcQwggHABgkqhkiG9w0BBwagggGxMIIBrQIBADCCAaYGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMt3UXikOCMbFFo3uBAgEQgIIBd_nyeXRk9jT_8rcQbWqa_BbjOsS9OycfEcsl35dz2p82CJWMYINH6k_wS_hesNlGnvKS44HnGtMS3FPAEfSp6OPboMJyoHS6e27dgZ8_aGrTF8Pg0vgTsQKxLWDaPmaCeVV2vcmJ7TL_SWUuA7Z9PPxFlkS9XtKknsWvIs0l6IpvkP1iVEhj0QTwCGRRopsLdvdsPPWkAD4mqjohLUf7UlFEZrP3h70MzOk0U1FwGffXPd094_k6QxLWqg1zv6fX7jXOv41GBFxJjMTqFb5vIZUOzG0IVhxcCu0AxFLCV74Po8FZLePH0UXh2Y9zKiSclmhRajhdDA7RyQ59SLjqGsDOReSjw5AathvDmdseel04X3yB98iyIx1QMo2F9mosKnJPZbzZnnaEnnFHVAUpzH-phESAT0T6jW22OrzwWU-hDKb1pSetLkETkrprd9AE0vOrqbak-HWpi_ne2xPbAkSPgYLkflPCEdQ2l5L1SglFNucbwJc2zg

[xidianbill]

I know there are some tools to predict the subcellular localization. But I want to know the specific ratio of proteins in different cellular compartment. And the last link can't work anymore. Do you mind tell me the book title?

[natasha.sernova]

This is not a book, this is an article with many citations. https://scholar.google.ru/scholar?hl=ru&as_sdt=0%2C5&q=BaCelLo%3A+a+balanced+subcellular+localization+predictor+Andrea+Pierleoni%2C+Pier+Luigi+Martelli%2C+Piero+Fariselli+and+Rita+Casadio+%01&btnG=

Concerning the specific ratio of proteins I am afraid it is species specific, tissue specific and protein specific.

There are about 50 articles about the ratio you need:

https://scholar.google.ru/scholar?hl=ru&as_sdt=2005&sciodt=0%2C5&cites=12103858286390794897&scipsc=1&q=protein+ratios+in+different+cellular+compartments&btnG=

[xidianbill]

Yeah, the ratio of protein is various among species and themselves, even among cell types. But it seems that there is not any algorithm that can predict the ratio of proteins. So I wonder if there are some high-throughout techniques that can measure the protein content, like RNA-seq for RNA, and if there are some data sets that fractionized the cell into different compartment and test the content respectively.

Answer 1

[Jean-Karim Heriche]

The state of the art for measuring intracellular protein concentrations is fluorescence correlation spectroscopy. To see how this can be done for multiple subcellular localizations, have a look at our bioRxiv preprint describing how we built our mitotic cell atlas.