Recently, Yang et al. reported that estrogen receptor beta (ER beta) is a mitochondrial protein rather than a nuclear receptor. Because this claim would lead to a significant change in our understanding of estrogen signaling, we have attempted to reproduce the MALDI-TOF data of Yang et al. We separated proteins extracted from mouse liver mitochondria by SDS-PAGE and analysed a gel band covering the molecular weight range of 50-65 kDa by MALDI-TOF/TOF. Analysis of the data with the MASCOT database algorithm provided no evidence for the presence of ER beta in the mitochondria. If we search (as the authors did) with only the peptide masses which match to tryptic fragments of ER beta, ER beta is identified with a significant score of 69. However, fragmentation of these peptides shows that they are not from ER beta. Our conclusion is that ER beta cannot be identified by MALDI-TOF from a mixture of mitochondrial proteins resolved on SDS-PAGE. (c) 2006 Elsevier Inc. All rights reserved.