Impact of injection solvent composition on protein identification incolumn-switching chip-liquid chromatography/mass spectrometry

In shotgun proteomics, the gold standard technique is reversed-phase liquid chromatography coupledto mass spectrometry. Many researches have been carried out to study the effects on identification per-formances of chromatographic parameters such as the stationary phase and column dimensions, mobilephase composition and flow rate, as well as the gradient slope and length. However, little attention isusually paid to the injection solvent composition.In this study, we investigated the effect of the injection solvent on protein identification parameters(number of distinct peptides, amino acid coverage and MS/MS search score) as well as sensitivity. Trypticpeptides from six different proteins, covering a wide range of physicochemical properties, were employedas training set. Design of experiments was employed as a tool to highlight the factors related to thecomposition of the injection solvent that significantly influenced the obtained results. Optimal resultsfor the training set were applied to analysis of more complex samples. The experiments pointed outoptimising the composition of the injection solvent had a strong beneficial effect on all the consideredresponses. On the basis of these results, an approach to determine optimal conditions was proposed tomaximise the protein identification performances and detection sensitivity.