MS/MS visualizer

Description

This tool displays a three-dimensional plot of the MSn data. The are 4 options for X and Y axes: retention time, precursor ion m/z, product ion m/z, neutral loss and 3 options for Z axis: precursor ion intensity, product ion intensity, retention time. You can filter ions by the product intensity and select ions for diagnostic fragmentation filtering in parameters. Also module enables you to highlight values of interest and sort ions by Z value.

Diagnostic fragmentation filtering

Due to common structural features, compounds within the same class undergo similar MS/MS fragmentation and as a result of many identical product ions and/or neutral losses. Diagnostic fragmentation filter (product ion filter) is a post-acquisition approach to screen LC-MS/MS datasets for entire classes of both known and unknown natural products. This tool searches all MS/MS spectra for product ions and/or neutral losses that has defined as being diagnostic for the entire class of compounds. In other words it screens LC-MS/MS datasets for MS/MS spectra containing production ions and/or neutral losses that are specific to that class of compounds. The user defines the diagnostic product ions and/or the diagnostic neutral loss values (Da) to use in the filtering. The user can also define the minimum diagnostic ion intensity (% base peak) to use in the filtering.If a recurrent neutral loss occurs, a line pattern in the plot can be observed. If compounds carrying those diagnostic product ions and/or the neutral loss values are detected the resulting plot will show their product ion m/z and precusor ion m/z. Additionally, an output file may be specified that will output the results of the filtering. For a detailed view of diagnostic fragmentation filtering: Walsh, Jacob P., et al. "Diagnostic Fragmentation Filtering for the Discovery of New Chaetoglobosins and Cytochalasins." Rapid Communications in Mass Spectrometry (2018).

This tool is very useful to get an overview of large amounts of MS/MS data.

MS/MS Visualizer

Parameters

Raw data file
Selection of the raw data file to visualize. Only one file can be selected.
X axis
Selection of the X axis. There are 4 options:
Y axis
Selection of the Y axis. Options are the same as for X axis.
Z axis
Selection of the Z axis. There are 3 options:
MS level
MS level of the scans to be plotted.
Retention time
Retention time range.
m/z range
Range of m/z values for precursor ions in MSn scans.
m/z tolerance
Maximum allowed difference between two m/z values to be considered same.
Intensities filtering
Optional parameter to filter ions by intensity. There are 3 different options:
Diagnostic fragmentation filtering
Optional parameter for diagnostic fragmentation filtering described above. Has 2 subparameters: diagnostic product ions and diagnostic neutral loss values. Scans not containing any ion satisfying all input values will not be considered for the visualization.

Functionality

This plot is using the third part library JfreeChart for its basic functionality.