Best-matched internal standard normalization for LC-MS based metabolomics.
This code performs peak area adjustment based on the B-MIS (best-matched internal standard)
Targeted and Untargeted versions of B-MIS are in their respective directories with example input and output files.
Please cite the following paper when using this code: Boysen, A. K., Heal, K. R., Carlson, L. T., & Ingalls, A. E. (2017). Best-matched internal standard normalization in liquid chromatography-mass spectrometry metabolomics applied to environmental samples. Analytical Chemistry, acs.analchem.7b04400. https://doi.org/10.1021/acs.analchem.7b04400
Run the samples should be run in the following manner for the [quality control] (https://github.com/IngallsLabUW/QualityControl) and B-MIS.
- Standards run (all mixed) at least once at the beginning and end of the run, labeled: Date_Std_AdditionalID (e.g. 161018_Std_FirstStandardinH20)
- Standards run (in representative matrix, all mixed) at least once the beginning and end of the run, labeled Date_Std_AdditionalID (e.g. 161018_Std_FirstStandardinMatrix)
- Blanks run (preferably method/filter blanks) at least once labeled: Date_Blk_AdditionalID (e.g. 161018_Blk_FirstBlank)
- A pooled sample run at least three times throughout the run, labeled: Date_Poo_AdditionalID_Rep (e.g. 161018_Poo_PooledSample_1)
- Pooled samples run multiple times at both full and half strength is preferred in order to account for variability due to different sample matrix strengths.
- Samples, labeled: Date_Smp_AdditionalID_Rep (e.g. 161018_Std_FirstSample_BioRep1)
This code is written in R .
It requires the following packages available on CRAN:
- ggplot2
- tidyr
- graphics
- grDevices
- Hmisc
- gtools
- cowplot
- RColorBrewer
- xlsx
- readr
- stringr
- GGally
- dplyr
Jamie Collins and Laura Hmelo assisted in the development and release of this code. Thanks to four anonymous reviewers whose comments improved this method.
This project is licensed under the terms of the GNU General Public License v3.0. See the LICENSE file for rights and limitations.