Peptide-tight ESI/MSn analysis with segment of liquid chromatography effluent

Abstract

A segment flow protocol has been proposed for coupling nano-liquid chromatography (nano-LC) with mass spectrometry (MS) in peptide-based proteomics research. LC effluent was segmented by perfluorodecalin oil and stored as segments in sequence to carry out the following off-line MSⁿ analysis. In this way, incomplete identification of co-eluted peptides resulting from the MS scan rate, relatively slower than the LC elution rate, was solved to some extent for on-line coupling LC-MSⁿ analysis. The complex proteins from a sample of T. tengcongensis were successfully identified with one run using segment as the interface between nano-LC and MSⁿ analysis, compared to the total identified proteins with six runs using routine on-line nano-LC-MSⁿ analysis. This segment flow approach could eliminate detection loss and sample cross-contamination, providing a new method for peptide-based proteomic research, especially when the amount of sample is limited.