Shotgun proteomics of thermally challenged Caribbean reef corals (NCEI Accession 0227133)

A proteome profiling approach was taken to characterize the cellular biology of massive corals of the Upper Florida Keys exposed to experimentally elevated temperatures. Specifically, Orbicella faveolata specimens from two inshore (Cheeca Rocks & The Rocks) and one offshore reef (Little Conch) were incubated at either 33°C for 5 days or 32°C days for 31 days (with controls maintained at 30°C), and proteins were extracted from a subset of 16 samples (representing multiple coral genotypes at each temperature x time), separated by liquid chromatography, and sequenced by mass spectrometry (MS). The associated, open-access manuscript (Mayfield et al. 2021) includes all methodological details needed to interpret the proteomic data. However, I have nevertheless reiterated the majority of these details in this document to aid those in navigating the NCEI data submission. Alongside this detailed methodological treatise, I have also uploaded 16 RAW files generated by the MS (Q Exactive™, Thermo-Fisher Scientific [TFS]), 16 MZML (open-access MS mass peaks) files, 16 MZID (open-access MS results) files, two sequence libraries needed to query the proteomic data (fasta files for the coral host & its dinoflagellate [family Symbiodiniaceae] endosymbionts), and a tab-delimited “online supplemental data file” (OSDF) that 1) describes which samples were analyzed; 2) defines MS jargon and explains how to interpret the MS output; and 3) presents all data in a distilled format that is more amenable to analysis by traditional statistical approaches. Please note that there are 32 MZID files, rather than 16, because each of the 16 MZML files was separately queried against each of the two aforementioned fasta sequence libraries.