FragmentationAnalyzer A standalone Java tool to analyze MS/MS fragmentation data
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FragmentationAnalyzer Description

Fragmentation Analyzer is a Java-based open source instrument that can be used to analyze MS/MS fragmentation data. Nine different analysis types are supported: · Spectra Visualization - visualize the MS/MS spectra with fragment ion annotation, zooming and manual de-novo-sequencing. · Intensity Box Plots - analyze intensity variation for a set of identification of the same peptide. · Intensity Correlation - detect how the intensity correlates with the spread in intensity. · Intensity Meta Plots - further analyze the variations in intensity. · Mass Error Scatter Plots - visualize the mass error spread in a set of selected identifications/spectra. · Mass Error Bubble Plots - same as Mass Error Scatter Plots but with peak intensities added. · Mass Error Box Plot - analyze the variation in mass errors. · Fragment Ion Probability Plot - analyze the probability of observing specific fragment ions. · Fragment Ion Heat Map - compare fragmentation using heat maps of correlation data. Main features: Supports three input formats: ms_lims 7 Mascot Dat Files OMSSA OMX Files

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