Selenopeptide mapping in a selenium–yeast protein digest by parallel nanoHPLC-ICP-MS and nanoHPLC-electrospray-MS/MS after on-line preconcentration

Electrospray technique, Inductively coupled plasma/MS, LC/MS, Multiply charged ions, Peptides, Proteins.

ICP collision cell MS was optimized for the detection and retention-time marking of selenium-containing peptides in nanoHPLC (75 µm column) after on-line 100-fold preconcentration on a capillary (300 µm id) precolumn. The mobile phase composition, gradient and flow rate were chosen to allow electrospray-MS/MS to be successfully run in parallel in identical separation and preconcentration conditions in order to produce two matching sets of chromatograms: an element-specific one and a molecule-specific one. Knowledge of the retention time of a Se-containing peptide of interest allowed efficient data mining in the corresponding ES-MS chromatogram and the identification of minor Se-species. A third chromatogram was run to obtain collision-induced dissociation data for the target peptides. The performance of the method was demonstrated for a comprehensive on-line characterization of a mixture of peptides in a tryptic digest of a Se-containing protein fraction isolated by size-exclusion chromatography from a selenium yeast extract. The method allowed the identification of whole series of Se/S substitutions in individual peptides and, in some cases, sequencing of isomers differing in the position of selenomethionine residues in the amino acid sequence.