The code in this repository was used the generate the results appering in the article: Sarvin, B., Lagziel, S., Sarvin, N. et al. Fast and sensitive flow-injection mass spectrometry metabolomics by analyzing sample-specific ion distributions. Nat Commun 11, 3186 (2020). https://doi.org/10.1038/s41467-020-17026-6
There are two config files:
- configFile.m, which contains configurations for the entire flow-injection mass spectrometry analysis, including the parameters for detecting reproducible m/z features (also reffered in the code as significant).
- ConfigSamples.xml, which contains the information of the samples scanned (i.e. Samples and Blank file names format).
On the top of the script file you can find a section of the parameters for the script marked by: %%%%%%%%% Script parameters %%%%%%%%% It includes the path of the data and strings describing the analysis.
NOTE: In order to use this code a file named mzxmlread_my.m have to be created, which is a modified version of the original Matlab file named 'mzxmlread.m'. Comment out the following line (#465 in Matlab 2017b): out.scan = out.scan([out.scan.num]);
The raw data is publicly available in Metabolomics Workbench with the identifier ST001380 [https://doi.org/10.21228/M8P41V].