Online Nanoscale ERLIC-MS Outperforms RPLC–MS for Shotgun Proteomics in Complex Mixtures

We have explored the use of electrostatic repulsion hydrophilic
interaction chromatography (ERLIC) as an alternative to the gold-standard
in shotgun proteomics: reversed-phase (RP) LC for online ESI–MS/MS.
Conditions for sample solubilization and initial gradient conditions
were optimized to strike a balance between peptide solubility and
maximum peptide retention when using mobile phase with high organic
solvent concentration. Online ERLIC-MS demonstrated a 57% increase
in total peptide identifications compared to RP-MS. We examined the
mechanism of this improved performance and found that it stems from
ERLIC’s propensity to retain longer peptides, which can be
identified with greater confidence. Online nanoscale ERLIC-MS provides
a powerful new tool for enhancing MS-based shotgun proteomic in a
broad range of applications.