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Project container-simid

SIMID is a computer program, written in R, designed to read netCDF files generated by mass spectrometer in SIM (selected ion monitoring) mode, containing time courses of m/z spectra registered for various metabolites. It evaluates the peaks of mass isotopomer distribution (MID) of metabolites, thus preparing the data to further correction for natural isotope occurrence. The github repository "https://github.com/seliv55/simid" is used to create the docker image.

SIMID reads the CDF files presented in the working directory, finds the spectra corresponding to specific metabolites of interest; corrects baseline for each peak in the spectra; choses the time points where the distribution of peaks is less contaminated by other compounds and thus is the most representative of the real distribution of mass isotopomers in the analyzed metabolite; evaluates this distribution, and saves it in files readable by MIDcor, a program, which performs the next step of fluxomic analysis, i.e. correction of the SIMID spectra for natural isotope occurrence. The functions performed by SIMID are similar to those of RaMID (https://github.com/seliv55/ramid). However, there is a difference in the input data for both programs. Ramid uses the description of metabolites of interest provided in the format of the table, exchangeable with the database Metabolights. Therefore it designed for primary analysis of mass spectra already presented in this database and downloaded from it. Alternatively, SIMID is created for the initial step of analysis of recently obtained data that are not uploaded to Metabolights yet. The output SIMID provides in the format of the table, exchangeable with Metabolights, and also in a human-readable form. The difference in the format of input data description also determines an essential difference in the code. Input tables for RaMID provide the direct references to the CDF files corresponding to the information written in each line of the table. The input information for SIMID does not contain such a reference. The absence of reference simplifies the data description for the user but makes the code more complicated: it searches the desired spectra one by one through all the provided CDF files.
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