Improving Low Abundance Protein Identification in Complex Proteome Samples

NanoLC coupled with nanospray ionization (NSI) MS has become the standard for identification of low abundance proteins in complex proteomics samples. Although this technique provides sensitivity and resolution, the low flow rates used with this technique often result in long sample loading times, long gradient delays and long system re-equilibration times. The MS only generates useful MSMS spectra during the LC gradient time, resulting in MS utilization rates of only 20-50% of the total run time (inject to inject). This application note presents a method to increase the relative MS utilization time without impacting sensitivity or resolution.