Versatile Online−Offline Engine for Automated Acquisition of High-Resolution Tandem Mass Spectra

For automated production of tandem mass spectrometric data for proteins and peptides >3 kDa at >50 000 resolution, a dual online−offline approach is presented here that improves upon standard liquid chromatography−tandem mass spectrometry (LC−MS/MS) strategies. An integrated hardware and software infrastructure analyzes online LC−MS data and intelligently determines which targets to interrogate offline using a posteriori knowledge such as prior observation, identification, and degree of characterization. This platform represents a way to implement accurate mass inclusion and exclusion lists in the context of a proteome project, automating collection of high-resolution MS/MS data that cannot currently be acquired on a chromatographic time scale at equivalent spectral quality. For intact proteins from an acid extract of human nuclei fractionated by reversed-phase liquid chromatography (RPLC), the automated offline system generated 57 successful identifications of protein forms arising from 30 distinct genes...