xiFDR is an application for filtering crosslinked PSMs to a list of identifications with an attached confidence (False Discovery Rate).

The FDR 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. :

  • First the PSM level FDR.
  • Second the Peptide Pair Level FDR
  • Third the Protein Level FDR
    • the peptide pairs then get filtered to only contain the ones only containing proteins that passed the Protein FDR
  • Fourth the Link-Level FDR
  • Fifth the Protein-Pair-Level FDR

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 were 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)

  • Ensure java version 8 (64 bit) is installed on your computer (Note: when downloading with a 32-bit browser an explicit selection of 64-bit download is required).
  • For large scale analysis a computer with 16 GB memory is recommended.
  • Operating system: Windows (Windows Server 2008 and 2012 and Windows 8 and 10) and Linux (Debian 9, Ubuntu 14.04, Ubuntu 16.04) were tested successfully – but expect that any system running java 8 64 bit should suffice.
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