PNNL

Abstract

Capillary LC separation coupled with external accumulation FTICR mass spectrometry has recently been demonstrated to have significant potential for proteomics research. Accumulation of an excessive space charge in an external to the FTICR cell ion trap has been shown to result in increased mass measurement error, undesirable ion discrimination and/or fragmentation, and potentially causing misrepresentation or incorrect assignments of lower abundance peptides in the acquired mass spectra. In this work we report on the capability of data-dependent adjustment of ion accumulation times in the course of LC separations, further referred to as Automated Gain Control (AGC). Three different AGC approaches were evaluated based upon the number of putative peptides from a tryptic digest of four casein proteins detected in the course of LC/FTICR separations. AGC was found to increase by up to a factor of 3 the number of peptides identified compared to the conventional technique.