Compound-specific isotope analysis (CSIA) is the measurement of stable isotope ratios, such hydrogen isotopes (2H/1H) and carbon isotopes (13C/12C), in distinct organic compounds that have been separated from a complex mixture of molecules found in the environment. This tool is useful for tracing organic matter that comes from a source with a known isotopic composition (e.g., C3 plants and C4 plants have different photosynthetic pathways that result in large differences in carbon isotope ratios; precipitation and evaporation can change the hydrogen isotope ratio in water (e.g., water vapor generated by evaporation contains more 1H than 2H due to mass-dependent fractionation). Knowing how these processes produce distinct isotope ratios is key to answering questions about the hydrologic cycle and the carbon cycle, now and in the past.

To make compound-specific isotope measurements, we need to separate compounds of interest from a complex matrix of molecules that we sample from soil, water, and sediment. Here I briefly describe the procedure, but I recommend a few open source books to learn more about this topic:

Killops & Killops - Introduction to Organic Geochemistry

Zach Sharp's Intro to Stable Isotope Geochemistry

Step 1. Extract lipids from organic matter.

Step 2. Purify compounds of interest.

Step 3. Identify compounds using gas chromatography-mass spectrometry.

Step 4. Identify retention times for compounds of interest.

Molecules with smaller mass/charge ratio will pass through the column first, while larger columns will take longer to travel through the entire chromatography column. This results in different retention times for distinct compounds.
For compound-specific stable isotopes (e.g., d2H or d13C), we use a gas chromatograph coupled to an isotope ratio mass spectrometer (GC-IRMS) to measure the isotopic ratio of each distinct peak.

For compound-specific radiocarbon analysis, we need to physically collect the compounds as they exit the chromatography column. To do this, we attach a preparative fraction collector (PFC) to the GC outlet. We split the line so that a small fraction is still detected by the GC-FID, while the majority of the compound is transferred downstream to the fraction collector. We can install a glass u-shaped "trap" to collect the material eluted at specific retention times where compounds are detected.