Position-specific isotope analysis, also called site-specific isotope analysis, is a branch of isotope analysis aimed at determining the isotopic composition of a particular atom position in a molecule. Isotopes are elemental variants with different numbers of neutrons in their nuclei, thereby having different atomic masses. Isotopes are found in varying natural abundances depending on the element; their abundances in specific compounds can vary from random distributions (i.e., stochastic distribution) due to environmental conditions that act on the mass variations differently. These differences in abundances are called "fractionations," which are characterized via stable isotope analysis.
Isotope abundances can vary across an entire substrate (i.e., “bulk” isotope variation), specific compounds within a substrate (i.e., compound-specific isotope variation), or across positions within specific molecules (i.e., position specific isotope variation). Isotope abundances can be measured in a variety of ways (e.g., isotope ratio mass spectrometry, laser spectrometry,  NMR, ESI-MS). Early analyses varied in technique, but were commonly limited by their ability to only measure average isotope compositions over molecules or samples. While this allows isotope analysis of the bulk substrate, it eliminates the ability to distinguish variation between different sites of the same element within the molecule. The field of position-specific isotope biogeochemistry studies these intramolecular variations, known as “position-specific isotope” and “site-specific isotope” enrichments. It focuses on position-specific isotope fractionations in many contexts, development of technologies to measure these fractionations and the application of position-specific isotope enrichments to questions surrounding biogeochemistry, microbiology, enzymology, medicinal chemistry, and earth history.
Position-specific isotope enrichments can retain critical information about synthesis and source of the atoms in the molecule. Indeed, bulk isotope analysis averages site-specific isotope effects across the molecule, and so while all those values have an influence on the bulk value, signatures of specific processes may be diluted or indistinguishable. While the theory of position-specific isotope analysis has existed for decades, new technologies exist now to allow these methods to be much more common. The potential applications of this approach are widespread, such as understanding metabolism in biomolecules, environmental pollutants in air, inorganic reaction mechanisms, etc. Clumped isotope analysis, a subset of position-specific isotope analysis, has already proven useful in characterizing sources of methane, paleoenvironment, paleoaltimetry, among many other applications. More specific case studies of position-specific isotope fractionation are detailed below.