Talk:Proteome

Wiki Education Foundation-supported course assignment

This article was the subject of a Wiki Education Foundation-supported course assignment, between 27 August 2019 and 6 December 2019. Further details are available on the course page. Student editor(s): Danielajbq.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 07:21, 17 January 2022 (UTC)

X-ray spectrometry

Does anyone else feel that x-ray spectroscopy should be mentioned? I realize this isn't terribly popular right now due to the massive expense of equipment, but there is exciting progress being made. And it reveals more than mass spectroscopy, especially regarding structure. I think it'll be a big deal for proteomics, heme research has already seen significant gains.

Cell proteome vs organism proteome

The following is from the Proteomics page:

"The entirety of proteins in existence in an organism throughout its life cycle, or on a smaller scale the entirety of proteins found in a particular cell type under a particular type of stimulation, are referred to as the proteome of the organism or cell type respectively."

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I think the term "proteome" is in need of some conceptual clarification. It can make sense to tie the term to individual cells. It is in the context of a functioning network of transcription factors inside a cell that we can begin to make sense of why a particular set of genes will be expressed.

Science, Vol 270, Issue 5235, 369-370 , 20 October 1995 "Mission Impossible: Follow the changes taking place in a cell by identifying the thousands of different proteins the cell produces and watching how they ebb and flow over time. But a growing band of researchers believes that improved analytical techniques may soon make such an approach feasible, and they have even coined a new term for it: proteome research."

But it also makes some sense to conceptualize the sum total of all the individual cellular proteomes in an entire multi-cellular organism.

Biotechnol Genet Eng Rev. 1996;13:19-50. Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it.

Science, Vol 291, Issue 5507, 1221-1224 , 16 February 2001 "A single gene can encode multiple different proteins--these can be produced by alternative splicing of the mRNA transcript, by varying translation start or stop sites, or by frameshifting during which a different set of triplet codons in the mRNA is translated. All of these possibilities result in a proteome estimated to be an order of magnitude more complex than the genome."

The term "proteome" has also been used in the context of subcellular bilogical systems such as viruses.

J Proteome Res. 2002 Nov-Dec;1(6):501-13. "Analysis of the adenovirus type 5 proteome by liquid chromatography and tandem mass spectrometry methods. JWSchmidt 22:10, 28 Mar 2004 (UTC)

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To confuse things a little bit more the proteome of a genome is defined as the product of all ORFs. Mostly this is used for in silico studies, though. Splicing events are up to now rarely considered while discussing predicted proteomes (in conctrast to actual experimental studies, in which the genome is mostly only used for MS-based identification of the proteins). This is mostly due to the difficulties in predicting splicing events without experimental data. Anyway, I went ahead and changed the introduction a bit to accommodate the historical basis of this term, as well as added the hands-on definition used in most labs. I am still not quite happy with the following paragraph as it lacks a little bit in structure in my opinion CharonZ 13:34, 26 April 2007 (UTC)

Human Proteome Project section?

Should something be added about the status/history/etc of the Human Proteome Project? I'm not familiar enough with it to know how it relates to other things, but it seems a mention here would be appropriate, if only to say what it is not. Jimw338 (talk) 15:50, 2 February 2013 (UTC)

I added HPP and ProteomicsDB to the paragraph describing HumanProteomeMap project, and a reference to yesterday's paper in Nature Communications with over 90% of the predicted proteome covered with high stringency by the HPP. The page needs more work in placing these (and other) projects in proper context, and at least a mention of the different criteria used to claim the identification of a protein.

MagnusPalmblad (talk) 09:39, 17 October 2020 (UTC)

Size and contents

I think the sentence "The proteome is larger than the genome" is not correct. The genome is not defined as the ensemble of genes, but as all the genetic material of an organism. In humans, the genes represent ~1% of the genome, so I am not sure that the proteome is larger than the genome (probably not). — Preceding unsigned comment added by 82.146.216.153 (talk) 09:23, 7 July 2015 (UTC)

I think a better to say the proteome contains a higher number of proteins than the associated genes due to spliceforms, post translational modification (glycosylation, phosphorylation, etc) — Preceding unsigned comment added by 130.88.93.203 (talk) 10:28, 11 October 2016 (UTC)