Abstract
Recent advances in nanoscale separations and high-resolution mass spectrometry permit highly sensitive and accurate analyses of complex protein mixtures. Here, we describe improved methods for nanoscale multidimensional chromatography coupled to targeted mass spectrometry (tMS) to achieve ultrasensitive quantification of peptides in complex proteomes. The presented chromatographic system consists of capillary strong-cation exchange (SCX) chromatography column, from which peptides are eluted directly onto high-resolution reversed-phase (RP) analytical columns and nanoelectrospray ion source. SCX prefractionation is used to separate phosphorylated peptides, permitting their ultrasensitive quantification. Resolution and robustness of this chromatographic system, together with the orthogonality of SCX and RP separations, permit scheduling of large panels of targeted MS assays. This design also enables seamless scaling to three-dimensional separations, thereby enabling large-scale, ultrasensitive quantitative proteomics.