This tool displays a two-dimensional plot of the data in a Data Dependent Acquisition (DDA) or Information Dependent Acquisition (IDA) experiment. The x-axis corresponds to retention time of the ms/ms spectrum and the y-axis is the m/z value of the precursor ion of the ms/ms spectrum.
This tool is very useful to get an overview of large amounts of MS/MS data.
Double clicking on any data point will display the corresponding MS/MS spectrum.
The following zoom functions are available:
At the bottom of the plot, it is possible to add peaks from a peak list to the plot. These will show up as green lines.
Please make sure that a peak list is available for the raw data file otherwise the dropdown box will be empty.
At the right of the plot, the second button allows to toggle displaying of the data points for the peaks.
And the third button allows to toggle displaying of tool tips on the peaks.
The last button to the right of the plot provides search functionality for specific fragment ions in the MS/MS spectra. After entering the m/z of the ion, ppm tolerance, min intensity, if you are looking for a neutral loss ion and color in the dialog prompt, all data points which fulfil the criteria will be colored with the selected color and with the shade based on the normalization.