Waller Lashanda N, Shores Kevin, Knapp Daniel R
Department of Pharmacology and MUSC Proteomics Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA.
J Proteome Res. 2008 Oct;7(10):4577-84. doi: 10.1021/pr8001518. Epub 2008 Sep 9.
Shotgun proteomic analysis usually employs multidimensional separations with the first dimension most commonly being strong cation exchange (SCX) liquid chromatography (LC). SCX-LC is necessarily a serial process for preparation of multiple samples. Here, we apply a newly available tool, off-gel electrophoresis (OGE), for first-dimension separation of peptide mixtures from digests of cerebrospinal fluid (CSF), a complex and low total protein-containing sample. OGE first-dimension fractionation enabled identification of a total of 156 unique proteins compared to 115 identified in previous work using first-dimension SCX fractionation. OGE can be used to process multiple samples unattended with easy retrieval of the separated fractions. Thus, shotgun analysis using OGE as the first-dimension separation offers a significant advantage both in terms of sample throughput as well as increased numbers of identified proteins.
鸟枪法蛋白质组学分析通常采用多维分离方法，其中第一维最常用的是强阳离子交换（SCX）液相色谱（LC）。SCX-LC必然是一个用于制备多个样品的串行过程。在这里，我们应用一种新的可用工具——凝胶外电泳（OGE），对脑脊液（CSF）消化后的肽混合物进行第一维分离，CSF是一种复杂且总蛋白含量低的样品。与之前使用第一维SCX分级分离的工作中鉴定出的115种蛋白质相比，OGE第一维分级分离共鉴定出156种独特蛋白质。OGE可用于无人值守处理多个样品，并能轻松回收分离的级分。因此，以OGE作为第一维分离的鸟枪法分析在样品通量以及鉴定出的蛋白质数量增加方面都具有显著优势。
