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The Multi-Q protein quantitation procedure comprises three major steps .
(Step 1)Data analysis starts with conversion of mass spectrometry data files and database search results into our data formats for subsequent quantitation.
(Step 2)Based on the identification results and the MS/MS spectra, signature ions of the iTRAQ labeled peptides are selected, processed and quantified.
(Step 3)In the final step, protein ratio determination, peptides with low identification confidence are removed. This program filter s out peptide data outside the instrument's dynamic range after assessment of the experimental data prior to peptide ratio normalization. Then, the normalized ratios of quantified, non-degenerate iTRAQ peptides are weighted according to their peak intensities to calculate the average protein ratios.
The final protein quantitation results are exported to an output file in CSV (comma separated values) data format.