Today, commercially available mass spectrometers increasingly meet all the demands of the proteomics community including high throughput, high sensitivity, and significant fragmentation capability for sequence determinations. Therefore, proper sample preparation is often the most crucial step to obtain the necessary data, particularly when working with biological samples. Depending on the size, sample preparation techniques differ and have to be optimized empirically. This is particularly apparent at the single cell level. In this chapter, we describe protocols for the use of MALDI-TOF mass spectrometry to directly analyse the peptidome of single insect neurons.