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High throughput GC-MS methods for quantification of alkylresorcinols (AR), biomarkers of whole grain wheat and rye intake, in plasma and adipose tissue and their metabolites in urine were developed and optimised. Alkylresorcinols in plasma (200 mu L) and adipose tissues (10-50 mg) were extracted with diethyl ether, whereas main AR metabolites such as DHBA and DHPPA and newly identified metabolites in urine (50 mu L) were extracted with ethyl acetate after enzymatic deconjugation. All extracts were purified on OASIS-MAX solid phase extraction cartridges. Plasma and adipose tissue sample extracts were then derivatised with trifluoroacetic anhydride and reconstituted in undecane, whereas AR metabolites in urine samples were derivatised with BSTFA+TMCS (99:1, v/v, 100 mu L). Prepared samples were quantified by GC-MS (EI-SIM). Analysis of all compounds in the different matrices showed good selectivity, sensitivity, linearity, precision (<15% within and between batches), adequate recovery (75-108%), and short total run time (10-12 min). The methods developed are applicable to large-scale sample sets such as epidemiological studies. (C) 2015 The Authors. Published by Elsevier B.V.