Table of Contents
STEP 1
This tool can be either used in a LIMS or stand-alone. In the stand-alone mode you should either drag/drop your experimental spectrum as a tab-delimited text file or copy paste it (CTRL-V) while moving you mouse over the drop zone. The list of available spectra will be displayed in the table and you may click on one of them to display it.
STEP 2 (Automatic)
When loading the spectrum a peak picking is done that determine the position and width of all the peaks based on global spectrum deconvolution algorithm that was implemented in JavaScript.
The result of the peak picking appears in the spectrum as yellow vertical lines. Note that the top of the peak is determined based on the 3 highest point and does not have to match an experimental point.
STEP 3
When trying to deconvolute a mass spectrum it is required to define all the possible molecular formula. It is important to limit as much as possible the number of molecular formula to consider.
The molecular formula is defined based on:
In the Picture we show the parameters of the Ionic liquid demo
STEP 4
Possible MFs can be filtered based on DBE (double bond equivalent, unsaturation), charge and molecular weight. It is also possible to add more advanced filtering option by entering a JavaScript code that can use the following variables:
STEP 5
In order to improve the isotopic profile matching between theoretical and experimental data a few parameters should be properly set here. First, we have to set the authorized experimental mass error in ppm (typically <5 for Orbitrap). Secondly, Peak width calculation is done automatically and allows to predict the peak width based on the mass and lastly we authorized experimental relative peak intensity threshold (typically between 0.01-0.1).
In figure we show the ionic liquid example.
STEP 6
Add any other Custom MFs by a comma. They will be ionized as the ionization parameters aforementioned. Only charged molecules are displayed.
Step 7
Analyze the data by clicking the button. The analysis should finish in a few seconds.
Results 1
Mass spectra window displays the experimental data (in yellow) overlaid with the reconstructed normalized matched ions (in blue). We can select a single ion in the table view and it is going to be highlighted in this view (in red). It is possible to zoom in (left button), -zoom out (double left button) and show this window on the full screen (option bar at the top of the window). The content of this window can be either printed or exported as SVG file (option bar). The ionic liquid example is shown in the figure (left).
Resuts 2
The view is a summarizing table named List of the various species. It contains all the information about the identified ions. You can see the molecular formula, its ionization form, the modifications, the charge and the Experimental MS. Important values such as Percent (in %) and the Amount (total intensity) are also included in this view. For any of the ions, you can zoom and interact in the mass spectra view (Results 1). All the data presented in the table can be classified by any criterion with a simple click on the column header. You can also use the search bar in order to search faster an individual value or use it by range. You can also export the whole table as text file with Export Data button. The data showed in the left represent the ionic liquid example available from List of experimental spectra.
Resuts 3
The Info box window shows details for the table-selected ion such as its name, monoisotopic mass, molecular formula, composition and charge. The quantity expressed in % of the total identified peaks is also given
