Filter Settings
Processing Parameters
Additional settings can be set for the preprocessing of the identification files:
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e-value filtering: In order to reduce the memory consumption it is possible to remove identifications with a high e-values.
It is adviced to keep these values as high as possible in order to ensure that PSMs reach a PEP of 1. This can be verified in the Validation tab.
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Peptide Length: lower and upper limits can be set for the peptide length.
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Precursor Accuracy: The higher precursor mass error allowed can be set here in order to filter out outliers.
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Exclude Unknown PTMs: When using SearchGUI with a modification at a particular amino-acid
on a peptide terminus, X!Tandem will search this modification on every termini and amino acid. If you post-process your results with PeptideShaker using the
option Exclude Unknown PTMs, the PSMs presenting inconsistent modifications will be discarded. You can thus artificially obtain the desired
results although the modification is a priori not compatible with X!Tandem.
Leaving a field blank results in disabling the filter.
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