rich in the membranes of some bacteria ( 1 ) and in animal skin and secretions, for instance, in sebum ( 2 ), cerumen ( 3 ), and meibomian gland ( 4 ) of the human eyelid and in the Harderian gland of rodents ( 5 ). They are also produced by rumen bacteria and are a substantial constituent of rumen tissue and milk. We recently showed that BCFA constitute 2% of fatty acids in the United States milk supply ( 6 ). The most prevalent monomethyl BCFA have branching on the n-2 or n-3 carbons, referred to as iso and anteiso , respectively. Polymethyl BCFA arising in prenol lipids are also common, specifi cally phytanic and pristanic acids.The routine method of fatty acid analysis is to convert them from their nature lipid class into fatty acid methyl esters (FAME), which have superb characteristics on capillary gas chromatograph columns with respect to peak shape and baseline separation. The usual approach for identifying branching in iso or anteiso branched chain FAME (BCFAME) is to examine the electron ionization (EI) mass spectrum for losses corresponding to branching at the end of the molecule. Although this approach is satisfactory in many cases, peak intensities are often low and sometimes do not enable unambiguous assignment. For this reason, specialized esters that localize charge and enhance structure-specifi c charge-remote fragmentation, such as dimethyloxazoline (DMOX) and picolinyl esters, are typically prepared for EI-MS analysis ( 7,8 ). However, preparation of DMOX, picolinyl, or other esters requires derivatization chemistry beyond routine methylation. Specialized esters have chromatographic characteristics that differ from FAME, requiring customized chromatography; peaks change retention times, sometimes inverting compared with FAME; establishing correspondence between showed that the molecular ions of four BCFA methyl ester (BCFAME) yield highly characteristic fragments upon collisional dissociation using a triple quadrupole instrument. Here, we confi rm and extend these results by analysis using a tabletop 3-D ion trap for activated molecular ion EI-MS/MS to 30 BCFAME. iso -BCFAME produces a prominent ion (30-100% of base peak) for [M-43] (M-C 3 H 7 ), corresponding to the terminal isopropyl moiety in the original iso -BCFAME. Anteiso -FAME yield prominent ions (20-100% of base peak) corresponding to losses on both side of the methyl branch, [M-29] and [M-57], and tend to produce more prominent m/z 115 peaks corresponding to a cyclization product around the ester. Dimethyl and tetramethyl FAME, with branches separated by at least one methylene group, yield fragment on both sides of the sites of methyl branches that are more than 6 C away from the carboxyl carbon. EI-MS/MS yields uniquely specifi c ions that enable highly confi dent structural identifi cation and quantifi cation of BCFAME. Abbreviations: BCFA, branched chain fatty acid; BCFAME, branched chain FAME; CAD, collisionally activated dissociation; FAME, fatty acid methyl ester.