Deep Bottom-up Proteomics Enabled by the Integration of Liquid-Phase Ion Trap

In this work, a LPIT-reversed phase liquid chromatography-tandem mass spectrometry (LPIT-RPLC-MS/MS) platform was established for deep bottom-up proteomics. LPIT was used here as a robust and effective method for peptide fractionation. LPIT separates peptides based on their effective charges and hydrodynamic radii, which is orthogonal to that of RPLC. With excellent orthogonality, the integration of LPIT with RPLC-MS/MS could effectively increase the number of peptide and protein being detected. When analyzing HeLa cells, peptide and protein coverages were increased by ~89.2% and 50.3%, respectively. With high efficiency and low cost, this LPIT based peptide fraction method could potentially be used in routine deep bottom-up proteomics.