Submitted on March 28, 2008
Revised on April 28, 2008
Accepted on April 29, 2008
A novel chromatographic method allows online reanalysis of the proteome
Leonie F. Waanders, Reinaldo Almeida, Simon Prosser, Jürgen Cox, Daniel Eikel, Mark H. Allen, Gary A. Schultz, and Matthias Mann
Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Martinsried 82152
Corresponding Author: mmann{at}biochem.mpg.de
Liquid chromatography combined with electrospray ionization is widely used for direct analysis of polar and labile molecules by mass spectrometry (LCMS). The online coupling in LCMS is a major strength but also causes a principal limitation that each eluting analyte has to be analyzed immediately and is not available for detailed interrogation after the LCMS run. Here we develop a new chromatographic strategy, which removes this limitation. After column separation the flow is split, one portion is analyzed directly and the other is diverted to a capture capillary. After the direct LCMS run, the flow is switched and the portion stored in the capillary is analyzed (replay run). We describe a set up consisting of an analytical column, a splitting valve and a focusing column, which performs at full sensitivity and undiminished chromatographic resolution. We demonstrate three principal advantages of this system; nearly continuous MS utilization, duplicate analysis without requirement for additional sample and targeting of important but under-sampled features in the replay run.