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understanding Phenyx
Change the number of variable modifications
Three searches were performed in order to produce the next graph. In
addition to the settings described above, the following parameters were
tweaked:
Parameter
Job 1
Job 2
Variable
Modifications
Oxidation_M
Oxidation_M
PHOS
Cys_CAM
Job 3
None
Cys_CAM
FIGURE 4. The number of variable modifications increases the set of sampled
peptides, thus increasing the size of the search space. As the number of
theoretically modified peptides increases, the more up and left the curve is
displaced. In other words, the p-Value worsens for a given z-Score.
The increase in search space from Job 2 to Job 3 (i.e. searching for the
oxidation of methionine and the carboxy methylation of cysteine) is
about a factor of two to three which has a relatively small impact on the
p-Values. However, when a variable modification is added such as
phosphorylation that looks at the less common amino acids serine (S),
threonine (T) and tyrosine (Y), the search space increases significantly.
Phenyx Web Interface Manual
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