pfas-homologous-series
A quick and dirty script for making a list of PFAS homologous series from processed LC-HRMS data
Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
-
○Academic publication links
-
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (10.1%) to scientific vocabulary
Repository
A quick and dirty script for making a list of PFAS homologous series from processed LC-HRMS data
Basic Info
- Host: GitHub
- Owner: SRehns
- License: mit
- Language: R
- Default Branch: main
- Size: 13.7 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
PFAS Homologous series
A quick and dirty script for making a list of PFAS homologous series from processed LC-HRMS data. I had previously done a brief search on GitHub to see if there was a quick script for this somewhere, as I did not find it I wrote one myself and here it is for other PFAS researchers to use at will.
Installation and setup
The code uses only base R so no additional packages are necessary to run this code. Simply download the R-file and open it in R-studio
Intended use
The code is customized to look for CF2 and C2F4 homologues in a data frame which contains at minimum retention time, kendrick mass defect, m/z or molecular weights. More homologous may be added in the future, such as CF2O-homologues.
The conditions in the code are as following: an increase in molecular weight corresponding to either CF2 or C2F4 (with a 0.001 Da tolerance), retention time must increase with molecular weight, Kendrick Mass Defect must be within a 0.001 tolerance.
The code will also calculate the ppm difference between "Compound 1" and it's potential homologue. Keep in mind that two out of three values in that calculation are experimental values which may inflate the ppm value.
Preparation
In any software which has processed LC-HRMS data, perform QC of sample data to ensure that only high quality peaks are included. Export the remaining compounds and then import them into R.
The line 'df <- Compounds_nodiscredited' will need to be modified so that df only takes in whatever you named the excel file that is being imported.
The line 'df1 <- df[c("Calc. MW", "m/z", "RT [min]", "Mass Defect: Kendrick MD [C F2]")]' will also need to be modified so that the column names align with your imported document.
Created by
Svante Rehnstam - Swedish University of Agricultural Sciences (SLU), Department of Aquatic Sciences and Assessment. 2023-03-30
Owner
- Login: SRehns
- Kind: user
- Repositories: 1
- Profile: https://github.com/SRehns
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: PFAS Homologous Series
message: Please cite this repo if used for a research publication
type: software
authors:
- given-names: Svante
family-names: Rehnstam
email: svante.rehnstam@slu.se
affiliation: Swedish University of Agricultural Sciences