Talk:Proteomics

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

And while I'm at it: 1) its not just having a difference in protein expression between different cells, its having a difference in the protein compliment of the cell; different proteins are present in different cells, and at different amount, and even the activity of the proteins can also be different. 2: we are looking at how proteins interact with each other and with the genome to produce a phenotype that is appropriate for the environmental conditions that the cell or organism finds itself in. 3:  I suggest that we not get into a discussion of what a gene is when discussing the proteome.  I think that our traditional definition of a gene is pretty troublesome and will probably be revised over the next few years. We can say that there are fewer transcribed regions that code for proteins than was expected (although I think 22k might be low).

--srlasky 04:21, 2005 Jan 11 (UTC)

I also have an issue with the statement "mass spectrometry and microarray produce peptide fragmentation information but do not give identification of specific proteins present in the original sample". This is exactly what mass spectrometry based proteomics does, often indirectly via peptides (see bottom-up proteomics), but also directly, as in top-down proteomics. Top-down proteomics is proteoform-specific.

MagnusPalmblad (talk) 12:24, 12 February 2018 (UTC)

Grammar in lists
(Reformatted by Pgan002 04:41, 25 February 2007 (UTC))

Then there is a point on good grammar; bulleted points should use the same kind of verb. for instance, this is what is in the article:


 * key technology
 * 1-D electrophoresis and 2-D electrophoresis are for the separation and visualisation of proteins.


 * To identify and characterise proteins mass spectrometry, X-ray crystallography, and NMR are used.


 * To characterise protein-protein interactions, a number of chromatography techniques are used especially affinity chromatography. Protein expression systems like the yeast two-hybrid and fluorescence resonance energy transfer (FRET) can also be used to characterise protein-protein interactions.

this is what it should be


 * Key technologies
 * 1 and 2 dimensional elect. are used to identify the relative mass of a protein and it isoelectic point.


 * Xray crystalography and NMR are used to characterize the 3D structure of proteins.


 * Tandem mass spect combined with reverse phase chromatography or 2D gel electrophoresis is used to identify and quantify the total protein found in cells


 * Affinity chromatigraphy, yeast two hybrid techniques, and Surface Plasmon Resonance are used to identify protein-protein and protein-DNA binding reactions.

I think I'll just add that, but note the parallel verbs used in the 4 points.

srlasky 04:21, 2005 Jan 11 (UTC)

Deleted text about approaches to proteomics
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)

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)

new "branches of proteomics"
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)
 * 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)

Recent change to caption of protein pattern analyzer
I'm the person who uploaded Image:Protein pattern analyzer.jpg from cancer.gov, and I've reverted a change made by 67.170.82.217 to this picture's caption. Personally, I'm unqualified to assess the accuracy or efficacy of the ECAN Genesis 2000, and I'm aware that captions on NIH pictures have been known to contain inaccuracies; however, to see a user with a limited edit history so radically alter a block of text makes it seem suspect to me. Compare the descriptions:
 * Original caption: ECAN Genesis 2000 robot preparing Ciphergen SELDI-TOF protein chips for proteomic pattern analysis. Highly accurate cancer prognosis can be accomplished by identifying protein patterns of specific cancers using this device.
 * Caption after edit by 67.170.82.217 (changes shown in bold): ECAN Genesis 2000 robot preparing Ciphergen SELDI-TOF protein chips for proteomic pattern analysis. Although many have tried, only highly in-accurate cancer prognosis can be accomplished by identifying protein patterns of specific cancers using this device, and its use in any clinically relevant application or research program is highly questionable.

If discussion on this page indicates some consensus that the accuracy of protein pattern analyzers is questionable, then I'm perfectly okay with it. Please understand, 67.170.82.217, that I don't mean to merely disregard your change, but instead want to vet it given that such a significant change has been made with no references or supporting argument.

-Quintote 11:37, 4 October 2006 (UTC)


 * I haven't really done any research on this but to my understanding the prognosis of cancer with proteomics has a real mixed history. In addition I believe that in particular some SELDI based research has proven to be unreproducible. A statement has been added about it this particular instrument being "the laughing stock of what is now considered the dark ages of proteomics". I don't think that is too far from the truth although a very unencyclopedic way of saying it. To my understanding it is a prime example of an over-hyped and over-promised technology platform that missed its mark by a long shot. There was also a highly cited and heralded MADLI-TOF study of ovarian cancer diagnosis back in about 1999 by Petricoin et al. in The Lancet that used some fancy neural networks or something which ended up being seriously flawed. This set off a series of studies that were really poorly validated that were designed for the same ends. I have not stayed up with the level of sucess but there are certainly ways to approach the same level of predictive power as traditional tests using very focused mass spec based proteomics but then you might not call it proteomics. In any case the "dilute and shoot" (unfocused, little sample prep) approach has generally been a failure. I would say that both statements above are off the mark but then again it is a caption. How about:
 * ECAN Genesis 2000 robot preparing Ciphergen SELDI-TOF protein chips for proteomic pattern analysis. Cancer prognosis by identifying protein patterns of specific cancers using devices such as this is an emerging field with a mixed track record of success.
 * Again I have not doen any real research on this but I beleive this is a more accurate and encyclopedic statement than either of the others.--Nick Y. 17:27, 4 October 2006 (UTC)


 * Thanks for giving this some insight, Nick. My sole concern is that the quality of Wikipedia is raised or maintained.  Bold edits should be encouraged, but not at the expense of verifiability.  I'm not hung up on getting references to peer-reviewed publications stating this, though obviously that's the desired goal; I just want a credible-sounding rationale for NPOV wording, and you provided that.  -Quintote 03:28, 5 October 2006 (UTC)

I partly agree with the criticism of the SELDI-TOF MS platform, the technology has low sensitivity and low reproducibility. However, there is now a growing research area within proteomics, which is sometimes referred to as "MALDI-TOF MS protein profiling". This research uses not only SELDI-TOF MS but also the similar platform from Bruker-Daltonics (here samples are prepared by magnetic beads) as well as several other variants combining sample treatment and MALDI-TOF MS quantification. Other biotech companies are currently releasing similar platforms (fx Perkin Elmer). To state that this research has generally been a failure is clearly wrong.

Often this kind of research identifies highly abundant fragments of plasma proteins in serum for potential use in clinical diagnostics. The actual clinical impact is yet unknown.

I suggest therefore removing the reference to Ciphergen Biosystems, since it is only one among several MALDI-TOF MS protein profiling platforms. In stead include a description of "MALDI-TOF protein profiling". —The preceding unsigned comment was added by 80.164.177.134 (talk • contribs) 11:27, 23 October 2006.


 * MALDI based systems are by far more reproducible than SELDI systems. There is nothing inherently wrong with either of these systems the issues of the past had more to do with the claims made than anything else. MALDI is an absolutle wonderful technology but is not the most reporducible thing in the world and requires expert involvement to get reproducibility out of it. There is a major difference between instrument reproducibility and assay reproducibility. Maybe you need to run the assay three times under different different conditions averaging many laser shots and you can get very robust indicators. Another problem people had in the past was the choice of sample preparation schemes that tended to leave way too much abundant proteins around masking the signal from the more relevant proteins. There is no doubt in my mind that protein profiling by mass spectrometry is a viable approach to diagnostics and there are examples of successes to prove this but there are also examples of failures. The technology is fundamentally sound but requires well designed thoughtful and even sceptical approaches. I would agree that the ciphergen SELDI system should be removed as the poster boy for this type of approach. Be bold. The change is welcome.--Nick Y. 17:38, 23 October 2006 (UTC)


 * I think that sounds great as well. The picture, however, is of a machine preparing Ciphergen SELDI-TOF protein chips.  If this looks exactly like a MALDI-based system, then I'd be okay with changing the caption, but I'd be concerned about misrepresenting the picture.  However good or bad SELDI-TOF profiling may be, that's what's in the picture. -Quintote 23:43, 23 October 2006 (UTC)

We agree that the picture of SELDI should be removed. It would be better to show a picture of another, less controversial, MALDI-TOF MS platform. In an article about cars you would show a commen and well tested car, rigth? Find a picture of a Bruker Daltonics MALDI instrument.

However, the statement "MALDI based systems are by far more reproducible than SELDI systems." is wrong. The average CV of the m/z is below 0.1% with SELDI as it is with all current MALDI protein profiling platform. Yes, you can get MALDI platform that are 10 times more mass accurate but these cannot be used in protein profiling, where a robust instrument design is desireable. And more importantly, the m/z ratio is of less importance in protein profiling. Here it is the reproducibility of the "peak intensity" that is of interest. No other MALDI platform has been shown to be more reproducible with respect to the peak intensity than SELDI (however, the variation is in general very high for all platforms). The problem in MALDI is not the instrument, the general problem is the variation inherent in the matrix-protein co-crystallization step, which is common to all MALDI platforms. The often heard statement that the SELDI instrument is a poor MALDI instrument is clearly wrong, and is argued by people who are not working with protein profiling but with other types of MS research.


 * The m/z "reproducibility" (accuracy) is dependent on the mass analyzer not the ionization technology, although in some systems the interface between the two is important (delayed extraction, etc.). Most common systems are TOF based. SOme of these newer TOF are quite impressive. You throw an FTICR on the back end and you have thousands or times more m/z resolution. Yes, MALDI signal intensity is largely dependent on the MALDI plate preparation (co-crystalization). I was including that in "instrumental parameters" as opposed to assay reproducibility. An assay can be developed around this reproducibility issue giving an accurate diagnostic. This, however, is a major issue and regulators are generally hesitant about diagnostics on such platforms. I said before there is nothing inherently wrong with SELDI. My statement about MALDI being more reproducible was more directed at a historical perspective. I should have said "have been". To my understanding the failures of the SELDI system had more to do with experiment design and the claims being made. Again I have not thoroughly researched this, but that is my understanding. Please give greater insight to this if you have some. I have seen excellent reproducibility out of MALDI systems but in the hands of a single expert, under well controlled and designed conditions. There is still an art to it. Internal validation with check samples etc. is important to any robust method. You must agree that SELDI has developed a negative reputation deservingly or not based on some high profile failures. MALDI has a good reputation which is often even over estimated, despite some major failures. Both techniques are often misunderstood. It is easy to reach false conclusions and design worthless experiments on both if the nature of the techniques are not understood. I really don't know that much about SELDI and would love for some one to write an article about it. Surface-enhanced laser desorption/ionization--Nick Y. 17:13, 24 October 2006 (UTC)

I think we agree after all. I am perhaps a bit more sceptical about reducing the reproducibility of the peak intensity simply by using well controlled and well designed experimental set up. I have seen studies of fully automated MALDI-TOF MS protein profiling experiments (fx sample loading and matrix application by robots), which in my mind do not show significantly improved reproducibility as compared to manual studies. However, this is difficult to conclude about, since the variation differs dramatically between individual protein peaks (presumably due to the physical/chemical properties of the primary sequence of individual proteins?). I think we need research in how to reduce the empirical nature of the crystallization step. There should a place in the history books for the person who solves that problem?

Great idea about a SELDI article.

—The preceding unsigned comment was added by Jakob A (talk • contribs) 13:29, 24 October 2006.

Number of human proteins

 * "... 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)


 * 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)

Need expert to restructure article
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)
 * 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)
 * 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)

=
================================= Not sure where I should add this point, but the first line of this text says "Proteomics is the large-scale study of proteins, particularly their structures and functions". Are there any experts that can either add the branches and technologies which address "function", or may be function should be taken out of the first line of the description of proteomics. The fact that function is mentioned high-up, but then not really addressed in detail could be very confusing to anyone using this text as a resource?

=
=================== 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)

Actually after re-reading I found that there are even more issues within this text. One problem that might be is that proteomics (as one of the "cool" omics) has been used rather liberal and sometimes in contexts that are not within its original definition. E.g. "The proteome of an organism is the set of proteins produced by it during its life" this is insofar wrong as the proteome (or proteome analyses, respectively) is the content of the protein at a given time point. As of now there are no possibilities to trace the proteome of an organism online (even time courses experiments consist of sampling at specific time points). In contrast, online in vivo analyses of certain tagged proteins are possible, but this is not proteomics anymore. If there are no objections I will make a major revision of the article in the next weeks CharonZ 08:54, 26 April 2007 (UTC)

=
================================= 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)

=
===========================================

I'm in the process of rewriting it from the beginning.

See what you think.

Gacggt (talk) 15:54, 14 June 2008 (UTC)

Okay, I'm done restructuring it... hopefully it is more readable now...

Gacggt (talk) 16:13, 14 June 2008 (UTC)

I have merged and restructured the sections on interaction proteomics. I have also added links to relevant other pages, and some citations where useful. I still think this section could be expanded slightly to include discussion of some current methodologies (also mentioned later in the article, perhaps more merging is called for?)

DevcomFellow (talk) 15:15, 25 February 2016 (UTC)

"Complexity of the problem"-Paragraph
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)

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

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