xiFDR is an application for filtering cross-linked PSMs to a list with attached confidence(FDR). This can be calculated on several levels:
PSM-level: Just straight on the input
Peptide Pairs: turns PSMs into unique peptide pairs and does the FDR estimation
Proteins: turns Peptide Pairs into unique Proteins and does the FDR estimation on Proteins
Residue Pairs: Peptide Pairs get folded up to unique residue pairs and the FDR is done on these residue pairs
Protein Pairs: Residue Pairs get folded up to unique Protein Pairs and the FDR is done on the Protein Pairs

One can define either a desired FDR for one of the levels or (under complete setting) define the desired FDR for each level.

When several FDRs are defined they will be applied in turn. :

Additionally one can enable "boosting" for a given level.

When selected the FDR of lower levels (e.g. for Link-Level these would be protein peptide pair and PSM) will be modified to maximise the number of results on the specified level.

If FDRs where defined for some of the lower levels then these will be taken as an upper limit. (e.g. if a 5% Peptide pair FDR was desired, the boosting will not increase that but at most select an FDR smaller then 5% for Peptide Pairs)

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