Here we report vibEELS in the scanning transmission electron microscope (STEM) to detect the vibrational signal of fluorine introduced in a trifluoromethionine (Tfm) amino acid, with high spatial resolution. Advances in electron-beam monochromation have enabled EELS to measure the molecular vibrational responses of materials but this has not been widely exploited for studies of biological systems. State-of-the-art monochromated instruments have energy resolutions of <5 meV (40 cm -1 ) and spatial resolutions ranging from tens of nanometers to the atomic scale , depending on the experimental geometry, making STEM-vibEELS a complementary technique to tip-enhanced scanning near-field optical spectroscopies . In contrast to conventional absorption spectroscopy, vibEELS measurements of molecular or biological systems often place the electron probe "aloof" from the surface of the specimen, without any direct contact of the electron probe with the sample. This experimental geometry exploits the long-range nature of the dielectric coupling of the electron beam excitation to the molecular vibrations and reduces electron beam damage . Aloof vibEELS has previously been used to study endogenous structural signatures in protein crystals , including isoform types and has demonstrated the possibility of isotope detection in labeled amino acids . This study uses the capabilities of STEM-vibEELS for tracking of spatially resolved, site-specific functional molecules introduced by 'zero-size', 'zero-background' chemical modifications. As a proof-of- principle system, we have used biochemical labeling techniques to incorporate fluorine into a methionine (Met) and applied STEM-vibEELS to measure the vibrational signal of the C-F bond.