Depending on the species examined, lipid droplets have been previously
reported to contain from 40 to 300 different proteins [39–43]. We
performed proteomic analysis on three biological replicates of N2 and
daf-2. Our lipid droplet proteome analysis confidently identified 354
proteins belonging to various functional classes including lipid metabolism,
other metabolism, transcription and translation, ribosome,
trafficking and transport, cytoskeleton, chaperones, and signal transduction
(Table 1, Table S2).
To estimate protein abundance we used a spectrum counting approach
[44] in which the number of MS/MS spectrum identifications
of the peptides belonging to a given protein were normalized (divided)
by protein length (Supplemental Table 2 and Table 1). For further analysis,
we focused on the top 100 most abundant proteins. The most
abundant protein was MDT-28. Even though this protein shares sequence
similarity to transcriptional mediator complex, it also contains
an N-terminal domain similarity to pfam 03036, which is a conserved
domain associated with the Perilipin family [10] (Supplemental
Fig. 1). Perilipins are conserved structural components of lipid droplets
that regulate lipid storage and hydrolysis [10