小中大我没有否定2D 技术, 有的paper基于2D做的非常好, 但是蛋白质组技术的发展很快, 2DGel和其他技术比较, 缺点更为突出, 所以期刊发表该类文章肯定考虑作者使用的技术, 使用2D技术的文章会影响编辑和审稿人对文章的评判. 我列出几篇2D技术缺陷参考文章：
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
4．最重要的一点， 用2DGel发现的biomarker往往在不同的疾病都是相同的，这些蛋白基本都是结构蛋白和高丰度的酶。即使发现到2000种蛋白, 信号分子,受体, 转录因子的比例也非常少. 如果你手头有2D结果可以比对。
Deja vu in proteomics. A hit parade of repeatedly identified differentially expressed proteins。Proteomics. 2008 May;8(9):1744-9.
TOP 15 most often identified differentially expressed proteins：
Human:
Keratins
Annexins
Peroxiredoxins
Actins
HSP27
Tropomyosins
GSTs
Enolases
PDIs
Tubulins
Cathepsins
TCP-1
Triosephosphate isomerase
Pyruvate kinases
Vimentin
Rodents:
Peroxiredoxins
Enolases
Tubulins
PDIs
Annexins
Actins
GSTs
Tropomyosins
Dihydropyrimidinase-like proteins
HSP60
Carbonic anhydrases
Apolipoproteins
ATP synthase beta subunit
Malate dehydrogenases
14-3-3 proteins
