BIOSSCOPE_targetedMtabs

12 April 2024
Krista Longnecker
Woods Hole Oceanographic Institution

The most important file here is the Excel file labeled KujawinskiWHOI_targetedMetabolites.2024.04.12.xlsx. The details are as follows:

• The data has New_ID as the leftmost column, and will have the same number of rows as the discrete data file that is available on the BIOS-SCOPE Google Drive as of January 5, 2024
• The remaining columns are the metabolites, one column per metabolite
• A matrix-matched standard curve was used to convert from peak areas to concentration
• The units for metabolites are pM
• The data are corrected for extraction efficiency, with the following exceptions
  • in the 2016 to 2019 there is no extraction efficiency information for:
    • 2-deoxyguanosine
    • hypoxanthine
  • 2021 data has no extraction efficiency for these metabolites:
    • 2-deoxyguanosine
    • hydroxypyruvic acid
    • hypoxanthine
    • myo-inositol
  • 2023 has no extraction efficiency for these metabolites:
    • cystine
    • glycine
    • hydroxocobalamin
    • hypoxanthine
    • lumichrome
    • nicotinamide
    • pantoic acid
    • beta-alanine (isom. alanine)
    • sarcosine
    • trigonelline
    • uric acid

The 2016 to 2019 data are already in the MetaboLights repository as MTBLS2356; these data are covered in the Longnecker et al. (2024) publication available here.

The data files here have metabolites that were detected during this project. There is a longer list of metabolites that were measured. Also note that these data are not corrected for limit of detection (LOD)/limit of quantification (LOQ). The data were collected on two different mass spectrometers, and the original TSQ showed changes in LOD over time. I decided to be as generous as possible and leave all possible values in here.

mfiles folder

There are three m-files in here because this part of the computer processing was done in stages.

• matchKujTargetedMetabolites_2016to2019.m --> used to convert the samples processed up to July 2019 into a format that matches the BIOS-SCOPE discrete file
• matchKujTargetedMetabolites_2021.m --> used to process the samples from July 2019 up through 2021; these are the final TSQ samples
• matchKujTargetedMetabolites_2023.m --> used to process the samples collected up through July 2023; these are the first Altis samples

dataFiles folder

This folder holds the MATLAB and Excel files that are either needed to merge in new targeted mtabolomics data, or are the output from prior merges.

Altis_processingFiles folder

These are the files used by Krista to read in and process El-MAVEN files
You should just need to edit riMAVEN.m to process one batch of samples after the El-MAVEN processing has been done. Hence this step of the analysis requires knowledge about the individual metabolites, how to use El-MAVEN, and how to use MATLAB.