MS Scripts

This script will subtract a blank background run from the run of interest, for example to ensure a good baseline for quantitation purposes, or to accurately measure differences between two or more runs. See also this chapter in the case that you have acquired the foreground and background in the same run.

Just follow the menu 'Tools/Report/Chromatogram Subtraction' and select the folders containing the datasets (foreground and background) and the applicable path masks. Once the script has run, it will generate a report with information about the impurities found:

First thing the scripts does is subtraction of the Analysis chromatogram (foreground) minus the blank (background), this will give us the real chromatogram we are interested in, which will only show peaks which are not in the background chromatogram.

To do this subtraction, it is necessary to align the spectra, and this will be done by introducing known peaks at the beginning and end of the run (they will use compounds with certain known very short and very long retention times, which they will introduce in the sample). Finally in the resulted chromatogram, the scripts does a peak picking and integration,  which will allow to identify impurity peaks (assumption is that this should be a pure compound, therefore the big peak is the compound, the others are impurities). The script continues until all impurities are check, and repeat process for every analysis chromatogram and its respective blanks. The script generates a Mnova document with the result in the Users folder and an output which is a set of tables as follows:

•Table with parent compound and impurities for analysis 1, with retention times and relative areas, as well as with the key ions which identify the impurity or parent compound

•Same table for subsequent analysis (2, 3, 4, etc.)

•Summary purity table, with averages from all analysis for each one of the peaks

Similarly to chromatogram subtraction, there is another script for UV subtraction (under the 'Tools/Report/UV Subtraction' menu). So you will subtract a background UV chromatogram from a foreground one:

The script located under the menu 'Tools/Export/Convert to Mnova Document" will allow you select the folder containing your datasets spectra, define a mask to set the name and extension of the target files and the folder where the Mnova documents will be saved. This script will be useful to convert MS formats (not compatible in Mac or Linux) from a Windows computer