Table 1. List of autophagy-related proteins identified by LC-MS-MS in media conditioned by serum-starved, caspase-activated EC (SSC) and serum-starved, caspase-inhibited EC (SSC-ZVAD).

No.	Protein identified by LC-MS-MS	Gene name	Function during autophagy
Predominant in SSC
1	LC3/Microtubule-associated proteins 1A/1B, light chain 3	MAP1LC3B	Autophagosome formation and expansion. Cytosolic and membrane-bound to autophagosomes.16,17
2	Cysteine protease ATG4D	ATG4D	Autophagosome formation and expansion. Cleaves the C-terminal part of MAP1LC3.16,18
3	Autophagy related protein 16-like 1	ATG16L1	Autophagosome formation and expansion. Associates with ATG12–ATG15 complex.19
4	VPS4 AAA ATPase/vacuolar protein sorting-associated protein 4B	VPS4/SKD1	Autophagosome formation and MVB biogenesis. Fusion of autophagosomes with endosomes and lysosomes.6,20
5	Vacuolar protein sorting-associated protein 16 homolog	VPS16	Formation and fusion of autolysosomes and endolysosomes.21,22
6	Lysosome-associated membrane glycoprotein 2	LAMP2	Fusion of autophagosomes with lysosomes.6,23
Predominant in SSC-ZVAD
1	Ras-related protein RAB7a	RAB7A	Fusion of autophagosomes and amphisomes with lysosomes.6,37