Readme file for data uploaded to data dryad project: Data from: Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Oceanfrom the Clarion Clipperton Fracture Zone

The data relates to the publication Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean Fracture Zone published in Marine Biodiversity.

DOI:https://doi.org/10.1111/1755-0998.13714

This dataset contains an Excel file called ReferenceTable.csv and a .zip file containing raw Bruker mass spectrometry files for 293 measurements from three species of Calanus. Of these, 114 measurements were carried out in a dilution series. Names of these mass spectra contain the dilution ration of the specimens (e.g. V1_1_64 means: extract from specimen V1 was diluted 1:64).
For each specimen, one folder is included in the .zip file. These files are named according to specimen names in the Excel file. The excel file also contains information on the accession numbers for DNA barcoded (COI) specimens. Furthermor the excel file contains sampling information such as sampling sites, longitude and latitude as well as depth.

The .zip file contains two folders named "Raw Spectra" and "Raw Spectra dilution series". These again are build up according to the default Bruker flex container system containing folders for each specimen. These folders are named accordingly. The "specimen folders" contain one folder for each spot that was measured for a specimen. Each "spot folder" consists of folders for each technical replicate measurement on the respective spot. Within these folders the actual data produced by the instrument can be found.


Data can be analyzed using Bruker proprietary software such as Bruker Flex analysis or Bruker Biotyper.

Alternatively, data can be analyzed in R using R-packages MaldiQuant and MaldiQuantForeign following the vignette that can be found via: 

https://cran.r-project.org/web/packages/MALDIquant/index.html
 
 
Additionally, the dataset contains three .html files which are R-scripts that can be used with the accompanied data to carry out analyses as presented in the associated publication.