This paper presents a protocol for applying flow cytometric (FC) sorting and direct temperature-resolved mass spectrometry (DT-MS) to oceanic particulate organic matter (POM) samples. Flow cytometric sorting allows the physical separation of particle subclasses on the basis of morphological and chemical criteria including size, shape, and autofluorescence characteristics. Direct temperature-resolved mass spectrometry is a rapid (~2-min) measurement that provides fingerprints of molecular-level characteristics across a wide range of compound classes, including both desorbable and pyrolyzable components. The resulting DT-MS data, therefore, can bridge the gap between information available from bulk measurements, such as elemental analysis, and information derived from detailed but laborious compound-class-specific analyses, In addition, the sensitivity of DT-MS (which requires only microgram quantities of sample (allows it to be used in conjunction with flow cytometric sorting. In this study, the sample-handling procedures required by these techniques are described in detail and shown to yield useful, representative results.