IP2 can compare fractionated biological samples in two different ways. Users can use either identification compare tool (see manual section 10) or the fractional analysis tool.
With identification compare tool, users need to upload each fractional data to separate experiment. Users can upload using a batch upload tool to automatically generate multiple experiments by one button. Users can submit search one by one, or run a batch search. After the search is complete, users can run identification compare tool to compare fractionated biological samples.
With fractional analysis tool, users need to upload all fractionated sample data to one experiment. Then submit one search before running fractional analysis. For fractional analysis, in general, we recommend uploading all data to one experiment and run one search and use fractional analysis tool, instead of uploading data to separate experiment and use an identification compare tool. With one search of all data, users can get statistically better results.
At the search result page, click ‘Fraction View’ link.
There are different options (radio buttons) for displaying data. All heat maps are based on a log10 scale from the spectral counts
default: spectral count display
Heat Map: Heatmap. The spectral counts are normalized by the maximum spectral count from all proteins.
Heap Map with spectral counts: Heatmap with the spectral counts. The spectral counts are normalized by the maximum spectral count from all proteins.
Heat Map Row Normalization: Heatmap. The spectral counts are normalized by the maximum spectral count from each protein (each row).
Heat Map Row Normalization with spectral count: Heatmap with the spectral count. The spectral counts are normalized by the maximum spectral count from each protein (each row).