I have an proteomic platform based on 2d electrophoresis and I get good answers for my scientific questions using it. Nowadays, gel-free proteomics seems to be prevailing over gel-based proteomics. Articles using two-dimensional electrophoresis are still being accepted for publication in reputable journals?
Hi Juliano,
2D gel-based proteomics has valuable features, e.g. its reproducibility and robustness. Nevertheless, 2D-PAGE based on isoelectric focussing (IEF) is technically limited because it is mainly restricted to soluble and/or high abundant proteins. In addition, 2D-PAGE is subject to restrictions, which include limited dynamic ranges and difficulties in
handling hydrophobic proteins and in detecting proteins with extreme molecular weights and isoelectric point (pI) values. The use of this technique very often leads to a relative low number of identified membrane proteins or lower identification in complex peptide or protein complexes. Therefore, alternative approaches (gel-free proteomics) are nowadays the more attractive choice for proteomic studies, but I think that for some specific scientific questions 2D-PAGE based proteomics is still acceptable.
Best regards,
Heidi
Hi Juliano,
2D gel-based proteomics has valuable features, e.g. its reproducibility and robustness. Nevertheless, 2D-PAGE based on isoelectric focussing (IEF) is technically limited because it is mainly restricted to soluble and/or high abundant proteins. In addition, 2D-PAGE is subject to restrictions, which include limited dynamic ranges and difficulties in
handling hydrophobic proteins and in detecting proteins with extreme molecular weights and isoelectric point (pI) values. The use of this technique very often leads to a relative low number of identified membrane proteins or lower identification in complex peptide or protein complexes. Therefore, alternative approaches (gel-free proteomics) are nowadays the more attractive choice for proteomic studies, but I think that for some specific scientific questions 2D-PAGE based proteomics is still acceptable.
Best regards,
Heidi
I don't think this is a question as much as this is an open topic to debate. It's not that journals are or are not accepting - it's more about what you make in order for journals to continue accepting it.
Personally, I think gel-pased proteomics alone answers some ecophysiological questions quite good: does the proteome change with a given external condition? how variable is the proteome of a species between individuals, from similar or different places/seasons/etc? Can we isolate only the proteins that are differentially expressed? Can we obtain a given amount of a given protein?
Unfortunatelly, you are right to recognize that journals do follow technological trends, often in a blind manner. It's a problem similar to that of impact factors - they are worthless indicators, but we have no way to run away from the importance that is being given to them.
Obviously, MS-based proteomics, either with LC- or gel-based protein profiling, allows further information to be obtained. But I think this should be critically asserted, rather than assuming MS is necessary for every study.
Hi Juliano,
To me the great advantage of 2D-Gels is the oportinuty to visualize and quantify full length proteins and to isolate different protein isoforms.
For large scale quantitative proteomics analyses, I moved to LC-MS/MS shotgun because of the limitations mentionned by Heidi. Shotgun is more sensible, the dynamic range is wider and you get access to any category of proteins. But the main limitation is that digested peptides from all protein isoforms are mixed all together. This makes very difficult the fine study of PTM for a protein of interest.
I still use 2D-gels for PTM analyses. The combination of 2D-gels with western blotting is very valuable to study the isoforms of a protein of interest. As long as your PTM induces a change in mass or charge, you can separate the modified proteins in the gels. In this way, you can pick up each isoform seperatly and get very precise information.
I think 2D-gel will still be valuable as long as Top-Down strategies remain difficult to handle on very complex samples.
There is no a simple answer to your question. I can only recommend you my review
paper that will help you in this issue https://www.researchgate.net/publication/310300442_proteomes_Towards_the_Full_Realization_of_2DE_Power
Article proteomes Towards the Full Realization of 2DE Power
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