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J Biomol Tech. 2007 February; 18(1): 53.
PMCID: PMC2291919

P154-S Simplified and Fully Automated Analysis of Complex Samples using LC-MSMS


LCMSMS is now a standard method for the analysis of protein samples which have been separated by 1D or 2D gel electrophoresis with subsequent in-gel digestion. However, the throughput is low as the analysis requires the use of long gradients and run times of over 30 min per sample. A more appropriate method is to analyze the samples without gel fractionation but this workflow is hindered by the ability of modern mass spectrometers to efficiently collect MSMS on all available ions when coupled with modern LC systems which produce very sharp chromatographic profiles. There is a growing trend towards resubmitting the samples after an initial analysis to collect data on ions which were initially missed.

Such a “repeat information dependant analysis” (rIDA) workflow is difficult to implement in an automated laboratory as the resubmission of samples with modified method automatically is cumbersome. This poster highlights the usage of an automated method/batch submission system which allows for unattended rIDA analysis.

A dramatic increase in the number of proteins which can be identified in a given sample was accomplished by coupling this automated workflow with easy-to-use database searching software. This highlights that repeated analysis of a sample consumed less material than using MudPIT based experimentation, and that a greater than threefold increase in the sample throughput can be achieved, without loss in quality of sample analysis using rIDA workflows.

Articles from Journal of Biomolecular Techniques : JBT are provided here courtesy of The Association of Biomolecular Resource Facilities