In this study, a novel method is presented by which the molecular environment of a transmembrane peptide can be investigated directly. This was achieved by incorporating a photoactivatable crosslinking probe in the hydrophobic segment of a model transmembrane peptide. When this peptide was incorporated into lipid bilayers and irradiated with UV light, a covalent bond was formed between the crosslinking probe and a lipid. This crosslinking reaction could be visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and the resulting product could be characterized by mass spectrometry. By use of phospholipases, it was demonstrated that the peptide crosslinks to both acyl chains of the lipids. The peptide showed a clear preference to partition into fluid lipids and was excluded from lipids in the gel phase. However, when the peptide was incorporated into bilayers containing two lipid species with different acyl chain lengths, molecular sorting of the lipids around the peptide based on hydrophobic matching was not observed. It is proposed that the size of the transmembrane part plays an important role in the dynamic interactions of membrane proteins with the surrounding lipids and hence in determining whether molecular sorting can occur.Proteins in biological membranes reside in a complex environment in which they are surrounded by many different lipid species. Transmembrane proteins can have different affinities for different lipids, and as a result particular lipids or members of particular lipid classes may become enriched around a certain protein. Such differences in affinity may be due to specific interactions with the lipid headgroups or the lipid acyl chains. An example of the latter would be the enrichment of matching lipids around a protein, which could be a mechanism by which mismatches between hydrophobic transmembrane segments and the hydrophobic thickness of the lipid bilayer can be relieved. Such a mechanism of molecular sorting by transmembrane proteins has been predicted from theoretical calculations (1, 2; reviewed in refs 3 and 4) and has indeed been shown to occur for several transmembrane proteins (5-8).To gain insight into the role of protein-lipid interactions in the sorting of lipids around specific proteins, tools must be available to determine the lipid environment of membrane proteins. Previously, this has been probed mainly by fluorescence and ESR 1 methods using labeled lipids (5-11). In this study, we explore a more direct method to investigate the immediate surroundings of membrane proteins. For this purpose we make use of a synthetic model peptide, which contains a photoactivatable probe that is able to form covalent bonds with the surrounding lipids upon UV irradiation. The crosslinking reaction can be visualized by SDS-PAGE analysis and the identity of the lipid that is crosslinked to the peptide can subsequently be characterized by mass spectrometry.