Recently, Schwend and Gustafsson tried to use the MALDI-TOF methods to confirm one of the results reported by Yang et a., which provided definitive evidences to demonstrate the localization of estrogen receptor beta (ER beta) in the mitochondria of multiple cell types, using immunocytochemistry, immunoblot, and proteomic approaches. Analysis of the data with the MASCOT database algorithm provided no evidence for the presence of ER beta in the mouse live mitochondria, in which very low ER beta expression has been detected in their own report. On the other hand, our MALDI-TOF analysis using human heart mitocliondrial protein has identified 7 and 8 sequences that could be potentially from ER beta and ER beta 3, respectively, but not from ATP synthases. Further, none of the sequences identified by us as those of ER beta and ER beta 3 shares m/z targeted by Schwend and Gustafsson in their measurements. Therefore, the claim by Gustafsson's laboratory about false positives in MALDI-TOF detection of ER beta in mitochondria has no relevance to our report. (c)\ 2006 Elsevier Inc. All rights reserved.