1.2D 技术发现的蛋白少：
Protein profile of the HeLa cell line J Chromatogr A. 2004 Jun 4;1038(1-2):247-65.
Approximately 3000 spots, excised from six two-dimensional gels, were analyzed. The analysis resulted in the identification of about 1200 proteins that were the products of 297 different genes.
2D+银染通常可以发现1000左右点，考染更少， 3000个点我相信是接近2D极限了， 发现的蛋白质（单一基因产物）只有不到300个。 最早的2DLC-MS发现的1500个蛋白, IEF + 1D SDS-LC/MS/MS 可以发现5000-6000蛋白. 从几百个蛋白和几千个蛋白筛选出来的候选蛋白的差别是显而易见的.
2。即使去除高丰度蛋白， 对2D的分辨率的提升也有限。
a. Serum biomarker discovery in renal cancer using 2-DE and prefractionation by immunodepletion and isoelectric focusing; increasing coverage or more of the same? Proteomics 2008 8:5074-5085.
Although this powerful prefractionation and analysis strategy allows the visualisation of multiple protein isoforms, it is insufficient to allow detection of lower abundance proteins in serum without the implementation of further strategies.
b. Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma. Proteomics 5:3292-3303
However, the number of new spots detected on 2-D gels was modest, and most newly visualized spots were minor forms of relatively abundant proteins.
3. 2D 定量受蛋白点重叠局限。
4．Spot overlapping in two-dimensional maps: a serious problem ignored for much too long。Proteomics. 2005 Jun;5(9):2385-95
事实上，现在SELDI和2DE做个profile就去投SCI的人基本上是自取其辱，怨不得杂志，这类人一般是没有好好读SCI文献，不知道自己和SCI的差距，前段时间也帮老板审过篇文章，也是2DE做个profile，鉴定出来一个差异蛋白，在功能讨论的时候居然张冠李戴说的是另外一个蛋白的功能可能有变化，所以我写到：your work may add some information, but mistakes should be corrected before, so rejected.作者: 大尾巴 时间: 2013-10-17 16:51
事实上，现在SELDI和2DE做个profile就去投SCI的人基本上是自取其辱，怨不得杂志，这类人一般是没有好好读SCI文献，不知道自己和SCI的差距，前段时间也帮老板审过篇文章，也是2DE做个profile，鉴定出来一个差异蛋白，在功能讨论的时候居然张冠李戴说的是另外一个蛋白的功能可能有变化，所以我写到：your work may add some information, but mistakes should be corrected before, so rejected.作者: 7437654 时间: 2013-10-17 17:04
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