There are no methods sensitive enough to detect enzymes within cells, without the use of analyte labelling. Here we show that it is possible to detect protein ion signals of three different H2S-synthesizing enzymes inside microglia after pre-treatment with silver nanowires (AgNW) using time of flight-secondary ion mass spectrometry (TOF-SIMS). Protein fragment ions, including the fragment of amino acid (C4H8N+ - 70 amu), fragments of the sulfur producing cystathionine-containing enzymes and the Ag+ ion signal could be detected without the use of any labels; the cells were mapped using the C4H8N+ amino acid fragment. Scanning electron microscopy imaging and energy dispersive x-ray chemical analysis showed that the AgNWs were inside the same cells imaged by TOF-SIMS and transformed chemically into crystalline Ag2S within cells in which the sulfur producing proteins were detected. The presence of these sulfur producing cystathionine-containing enzymes within the cells was confirmed by Western Blots and confocal microscopy images of fluorescently labelled antibodies against the sulfur producing enzymes. Label-free ToF-SIMS is very promising for the label-free identification of H2S-contributing enzymes and their cellular localization in biological systems. The technique could in future be used to identify which of these enzymes are most contributory.