Are there any secondary messengers involved in the lysosomal calcium signaling pathway?

Yes, nicotinic acid adenine dinucleotide phosphate (NAADP, Cat# 20999) is a Ca²⁺ mobilizing secondary messenger.  Like IP₃ and cADPR, NAADP binds to and opens Ca²⁺ channels on intracellular organelles. However, NAADP does not mobilize Ca²⁺ from the ER. Rather, it selectively targets and mobilizes Ca²⁺ from acidic Ca²⁺ stores such as endosomes, lysosomes, secretory granules and Golgi bodies. Recent research suggests that NAADP targets a family of membrane bound ion-channels, called two-pore channels (TPC), in order to stimulate Ca²⁺ release.

Since NAADP is negatively charged, it imposes difficulties when loading into live cells requiring invasive techniques such as microinjection, loading via liposomes or electroporation.  When assaying lysosomal Ca²⁺ signaling in live cells, use NAADP-AM (Cat# 20997), which is a cell-permeant analog of NAADP. It can easily penetrate intact cell membranes of live cells and induce NAADP-mediated calcium signaling.