Properties of ¹³C-Substituted Arginine in Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)

TLDR

The study investigates the use of fully 13C‑labeled arginine in the SILAC protein quantitation method. Cells were metabolically labeled with deuterated leucine, and 13C‑arginine–labeled peptides coelute with unlabeled counterparts in LC–MS/MS, allowing accurate quantitation and simplifying spectrum interpretation via predictable y‑ion shifts. The method yields a single C‑terminal label in half of tryptic peptides and enables accurate, reproducible quantitation of protein mixtures with relative standard deviations below five percent. Keywords: quantitative proteomics, peptide sequencing, protein identification, LC–MS/MS, cell culture, SILAC.

Abstract

We have recently described a method, stable isotope labeling by amino acids in cell culture (SILAC) for the accurate quantitation of relative protein abundances. Cells were metabolically labeled with deuterated leucine, leading to complete incorporation within about five cell doublings. Here, we investigate fully substituted 13C-labeled arginine in the SILAC method. After tryptic digestion, there is a single label at the C-terminal position in half of the peptides. Labeled and unlabeled peptides coelute in liquid chromatography−mass spectrometric analysis, eliminating quantitation error due to unequal sampling of ion profiles. Tandem mass spectrum interpretation and database identification are aided by the predictable shift of the y-ions in the labeled form. The quantitation of mixtures of total cell lysates in known ratios resolved on a one-dimensional SDS−PAGE gel produced consistent and reproducible results with relative standard deviations better than five percent under optimal conditions. Keywords: quantitative proteomics • peptide sequencing • protein identification • LC−MS/MS • cell culture • SILAC