Talk:Proteomics

message: (Reformatted by Pgan002 04:41, 25 February 2007 (UTC)
thread_title:  Contended facts from article 

message: Was the selection below deleted?  The 3D structure of purified proteins is a small part of proteomics, although it is a part of proteomics, and we are probably going to be able to find out a whole lot more about proteins by comparing the structure than by comparing their sequences.  For example, using round numbers, when we sequenced the Halobacterium NRC1 genome, there were more than 800 potential coding sequences that bore no sequence similarity to other known proteins (all the genes named with a vng in them are unidentified and are called vng... for Victor Ng, the lead scientist on the sequencing project).  By folding the predicted translation product of these unknown genes using ab initio technqiues and then comparing the 3D predicted 3D strututres, we were able to identify the function of more than 200 of the unknowns.  So these structural comparisons are important, but are only a small part of what we are getting from proteomics.
What I started to write about was the inclusion of the "environment" as being important in the proteome.  the article now states that the proteome is "constantly changing through its biochemical interactions with the genome and the environment. "  I'm not sure what that means.  How does the proteome biochemically interact with the genome?? and what part of the environment changes the constitution of the proteome? 
First, I just don't know what biochemical interaction takes place with the genome.  When proteins bind to the genome, they may be phosphorylated, but changes in phosphorylation are probably done before or after binding to DNA by autophosphorylation or by phosphorylation   by some other protein kinase:  for instance,  the JUN protein is phosphylated by the JNK protein and them then the P-JUN protein can bind to an AP1 site.  Dephosphorylation by protein phospotases is another important post-translational modification, but neither phosphorylation nor de-phosphorylation are catalyzed by the genome.  The genome pretty much is inert biochemically.  Its structure is changed by the alkylation, phophorylation, or other modification of DNA binding proteins, but the genome isn't doing it.
Second, what environment causes the proteome to change?  Environmental factors cause biochemical changes in the cells.  The cells can respond by changing the post-translational structure of preexisting proteins, or  environmental factors can cause a signaling cascade to  change the expression of genes leading to a changed proteome, but its not really the "environment" that is changing the proteome.  It is the cell responding to different conditions that leads to changing the proteome.  
I think that there is a better way to put the express how the environment causes the proteome to change, and I think it might be appropriate to retain the structural,  maybe using the kind of example I used above.
Before I do any of that, however, I'd like to see a comment on my misunderstanding of the term environment. It just sounds too wholistic the way its in there now.
thanks  srlasky 03:43, 2005 Jan 11 (UTC)
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This was deleted from the article by 64.230.7.80:
:Two major approaches to proteomics exist: the study of in-vivo samples and the synthesis of recombinant proteins.  In the second instance, genetic engineering techniques are used to clone the DNA template for the protein being synthesized and to splice these gene into host cells, typically bacteria, which are made to express the protein in large scale.
:The protein then has to be extracted from the host cells and purified.  Subsequently, the pure protein is submitted for crystallization (and then x-ray) or NMR for structural determination.  NMR is not effective for large proteins.
:Proteomics is a greater challenge than genomics because the 3-dimensional geometry of proteins is critical in their function.  It is important and challenging to preserve this geometry through all the steps described above.
some of this could be relocated to structural biology, but some of it probably deserves to be in this article.   64.230.7.80, please don't simply delete material, but move it to the relevant Talk page, or a more relevant article.  We try to preserve as much good well-written information on wikipedia (as the above paragraphs are), and if it's misplaced it should be relocated not simply deleted. --Lexor|Talk 08:54, 24 Apr 2004 (UTC)
thread_title:  Deleted text about approaches to proteomics 

message: I just added a new section on "branches of proteomics". This is my first major Wikipedia edit, so I'd appreciate feedback. The "proteomics" entry is very short now and I'm not happy with the layout. The "key technologies" section is very limited now, and I think it should be revised. What do you all think? Janbrogger 21:04, 21 Mar 2005 (UTC)
replies: text: I like your edits, As long as everything in key techs is coverd, go ahead and delete the key technologies section--nixie 22:54, 22 Mar 2005 (UTC)
thread_title:  new "branches of proteomics" 

message: : "... there are far fewer protein-coding genes in the human genome than proteins in the human proteome (20,000 to 25,000 genes vs. about 1,000,000 proteins). The human body may contain more than 2 million proteins, each having different functions."
How many proteins are there thought to be -- 1 million, 2 million or between 1 and 2 million?  Need references.  Also, the second sentence says that each protein has more than one function.  Is that true?  -Pgan002 04:27, 25 February 2007 (UTC)
replies: text: While the human genome can only code for the low tens of thousands of distinct proteins (some individual genes code for multiple, slightly different proteins), proteins can be altered after their initial formation.  The bulk of the distinct proteins will be antibodies, all coded for by a handfull of genes that have a manner of being altered during white blood cell production, allowing them to produce at least millions of distinct antibody protiens.  However, if we exclude antibodies, as well as proteins that differ only by what non-protein substances are bound to them, such as oligosaccharides, I would highly doubt the claim of millions of distinct proteins (this would require each protein to be altered in 100 different ways, on average), though I don't recall ever seeing a count in a text book or journal.  As far as each protein having more than one function, while this may be suspect, it is not proven.  Although here there is need to distinguish function and purpose; a protein will almost inevitably have more than one chemical function, but only be known to accomplish a single purpose, or possibly have no known purpose.  Someguy1221 20:35, 4 April 2007 (UTC)
thread_title:  Number of human proteins 

message: This article needs to be restructured and rewritten by someone who understands the subject well.  Many terms and concepts need to be introduced before they are used; much repetition needs to be removed; like information needs to be collected together.  -Pgan002 06:00, 25 February 2007 (UTC)
replies: text: Seconded. This article may be difficult to understand for the uninitiated. I work in proteomics, so may get around to it. But if anyone can recruit someone, go ahead... Janbrogger 19:01, 25 February 2007 (UTC)
replies: text: I have checked the article and did not found any obvious mistakes. It also looks sufficiently clear to me, despite probably too much wordy in some places. Audriusa 16:57, 8 April 2007 (UTC)
thread_title:  Need expert to restructure article 

message: Actually I am not sure whether the given article is well suitable to describe proteomics. Similar as genomics, proteomics usually refers to high-throughput systems to identify complete sets of expressed proteins in a given cell, tissue or organism. Much in the text does not put enough emphasis on this and gets distracted by a number of techniques. I think this is one of the reasons why the text appears to be too wordy and possibly less focussed than it might be.
I would suggest to start off with definitions in proteomics and focus on the goals that are to supposed to be achieved  by this methodology(e.g. systems biolgy), In addition maybe specific examples (papers) of certain milestones could be given-
Technologies should only described with respect to their importance for proteomics. For a number of techniques (MS, MS/MS, 2DE-page etc.) already better articles exist. The only more technological description that could be useful might be the workflow of standard experiments, but then it might be taking it too far. CharonZ 12:14, 16 April 2007 (UTC)
thread_title: ====================

message: May be somebody should write the article from beginning.
This article is very chaotic. I think that we have to change overall scheme of this article.
Maybe some standard parts like:
Short abstract/definition on the beginning (before TOC), than 
*Branches of proteomics identification, comparative proteomics, study of interactions, prot. structure etc.
*Technologies need rewrite? - there is a "mix" of different methods for different thinks
*Large scale protein identification - typical approaches to protein identification (2DE -> MS and shotgun methods - MudPIT)
*Applications of proteomics - here we can write sth. about markers, diseases, biotechnology
--Mkotl 15:33, 20 September 2007 (UTC)
thread_title: ==================================

message: I'm in the process of rewriting  it from the beginning.
See what you think.
Gacggt (talk) 15:54, 14 June 2008 (UTC)
thread_title: ============================================

message: The paragraph starts like this: "After genomics, proteomics is considered the next step in the study of biological systems." I'm wondering wether transcriptomics wouldn't be the next step after genomics. If transcriptomics should not be taken in consideration a reference for the first sentence might be necessary.
89.0.51.135 (talk) 20:14, 26 July 2010 (UTC)
thread_title:  "Complexity of the problem"-Paragraph 

message: First paragraph contradicts itself on date the phrase was first coined.  Buchs (talk) 15:29, 15 October 2012 (UTC)
thread_title:  Direct contradiction on coining of phrase 

message: Hello fellow Wikipedians,
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thread_title:  External links modified 

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