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This procedure is used to compute ratios of peptide and protein abundances and then to perform a statistical analysis. The significance of ratios varations is then computed at protein and protein levels using two statistical tests (T-Test and Z-Test). Several filters can also be set to increase the quality of quantitative results.
Here is the description of the parameters that could be modified by the user.
* Use only specific peptides: if checked, peptides shared between different protein sets will be discarded from the statistical analysis.
* Discard missed cleaved peptides: if checked, peptides containing missed cleavages will be discarded from the statistical analysis. It has to be noted that perfect tryptic peptides whose sequence is included in an observed missed cleaved peptide are also discarded if this option is enabled.
* Discard oxidized peptides: if checked, peptides containing the Oxidation(M) modification will be discarded from the statistical analysis. It has to be noted that non-modified peptides whose sequence is the same than an observed oxidized peptide are also discarded if this option is enabled.
par run en prenant une référence (1er run); sur la médiane de la distribution des ratios calculés entre chaque run et la référence
Peptide abundances can be summarized into protein abundances using several mathematical methods: