Code for manuscript "Large pool of organic ligands supports iron bioavailability and reduces copper toxicity in whale excrement" by Monreal et al.

.zip file containing GitHub repository titled "ligands-in-whale-excrement" (https://github.com/patrickmon38/ligands-in-whale-excrement/tree/main)

README from GitHub: 

Code used to generate figures for the manuscript "Large pool of organic ligands supports iron bioavailability and reduces copper toxicity in whale excrement" by Monreal et al. are found in this repository.

Most data (all except .mzXML data) called in code is from Github_Data_For_Whale_Ligand_Manuscript.xlsx in this repository.

Mass spec data from .mzXML files are has been depositied and is available for download in the Mass Spectrometry Interactive Virtual Environment (MassIVE). LC-ESI-MS (Orbitrap) and LC-FT-ICR-MS raw data can be accessed there under MSV000094994 (doi:10.25345/C50000B5D) and MSV000094995 (doi:10.25345/C5V98034P), respectively.

html output from Rmarkdown file can be viewed directly at https://html-preview.github.io/?url=https://github.com/patrickmon38/ligands-in-whale-excrement/blob/main/Figures_for_GitHub_Whale_Excrement_Manuscript.html.

If trying to run Rmarkdown on your own system, you will need to download the .xlsx and .mzXML files and change paths accordingly in lines 44, 87, 93, 456, 461.

Co-authors of this manuscript:

Patrick J. Monreal (University of Washington)
Matthew S. Savoca (Stanford University)
Lydia Babcock-Adams (National High Magnetic Field Laboratory)
Laura E. Moore (University of Washington)
Angel Ruacho (Univesrity of Washington)
Dylan Hull (University of Washington)
Logan J. Pallin (Unversity of California, Santa Cruz)
Ross C. Nichols (Unversity of California, Santa Cruz)
John Calambokidis (Cascadia Research Collective)
Joseph A. Resing (Unviersity of Washington/CICOES/NOAA)
Ari S. Friedlaender (Unversity of California, Santa Cruz)
Jeremy Goldbogen (Stanford University)
Randelle M. Bundy (Unversity of Washington)

If there are issues or questions with the code, author for contact is Patrick Monreal (pmonreal@uw.edu).