FragmentationAnalyzer is a standalone Java tool for analyzing MS/MS fragmentation data. Fragmentation Analyzer is a tool for analyzing MS/MS fragmentation data. Currently nine different analysis types are supported:
1. Spectra Visualization - visualize the MS/MS spectra with fragment ion annotation, zooming and manual de-novo-sequencing.
2. Intensity Box Plots - analyze intensity variation for a set of identification of the same peptide.
3. Mass Error Scatter Plots - visualize the mass error spread in a set of selected identifications/spectra.
4. Mass Error Bubble Plots - same as Mass Error Scatter Plots but with peak intensities added.
5. Mass Error Box Plot - analyze the variation in mass errors.
6. Fragment Ion Probability Plot - analyze the probability of observing specific fragment ions.
7. Fragment Ion Heat Map - compare fragmentations using heat maps of correlation data.
8. Intensity Correlation - detect how the intensity correlates with the spread in intensity.
9. Intensity Meta Plots - further analyze the variations in intensity.

Supports three input formats:
* ms_lims 7
* Mascot Dat Files
* OMSSA OMX Files

Requirements:
* Java

The license of this software is Free, you can free download and free use this application software.