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xiFDR specifications


Unique identifier OMICS_21714
Name xiFDR
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data An mzIdentML file or a table of PSMs.
Output data An amended mzIdentML file or a set of tables containing PSMs, peptide pairs, residue pairs, and protein pairs that pass the requested FDR thresholds.
Operating system Unix/Linux
Programming languages Java
License Apache License version 2.0
Computer skills Advanced
Version 1.0.10
Stability Stable
Source code URL https://codeload.github.com/lutzfischer/xiFDR/tar.gz/v1.0.10
Maintained Yes




No version available


  • person_outline Juri Rappsilber

Additional information


Publication for xiFDR

xiFDR citations


Capturing protein communities by structural proteomics in a thermophilic eukaryote

Mol Syst Biol
PMCID: 5527848
PMID: 28743795
DOI: 10.15252/msb.20167412

[…] ltration before LC‐MS analysis. All LC‐MS data were obtained from an Orbitrap Fusion Lumos Tribrid mass spectrometer (Thermo Scientific). Search and FDR were performed with the Xi (Giese et al, ) and XiFDR (Fischer & Rappsilber, ) software suites. […]


Optimizing the Parameters Governing the Fragmentation of Cross Linked Peptides in a Tribrid Mass Spectrometer

Anal Chem
PMCID: 5436099
PMID: 28402676
DOI: 10.1021/acs.analchem.6b04935
call_split See protocol

[…] earch databases consisted of a single entry with the sequence of the corresponding protein, that was extracted from the crystal structure PDB file (PDB IDs: 1AO6, 2CRK, 2FRJ). FDR was estimated using XiFDR on 5% residue level with enabled boosting and including only unique peptide-spectra matches (PSMs). To further minimize false positives in the target list, links with a distance >30 Å correspond […]


Blind testing cross linking/mass spectrometry under the auspices of the 11 th critical assessment of methods of protein structure prediction (CASP11)

Wellcome Open Res
PMCID: 5354267
PMID: 28317030
DOI: 10.21956/wellcomeopenres.10823.r18753
call_split See protocol

[…] ased on supporting PSMs). This provides a means to do noise filtering and can increase the number of unique residue pairs that pass a given FDR. Optimal score cut-offs are automatically defined using xiFDR: https://github.com/lutzfischer/xiFDR.The MS data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD003643 . […]


Optimized Fragmentation Regime for Diazirine Photo Cross Linked Peptides

Anal Chem
PMCID: 5047652
PMID: 27454319
DOI: 10.1021/acs.analchem.6b02082
call_split See protocol

[…] -link reactions were assumed to connect lysine, serine, threonine, tyrosine, or the protein N-terminus on the one end of the spacer with any other amino acid on the other end. FDR was estimated using XiFDR (v. on a 5% peptide spectrum match (PSM) level and 5% link-level only including unique PSMs. The reference database consisted of a single entry with the protein sequence of HSA (Unipro […]


A Study into the Collision induced Dissociation (CID) Behavior of Cross Linked Peptides*

PMCID: 4813691
PMID: 26719564
DOI: 10.1074/mcp.M115.049296
call_split See protocol

[…] to involve lysine, serine, threonine, tyrosine, and the protein N terminus. To ensure the analysis of high-quality data, we extracted 910 PSMs to unique cross-linked peptides at a 5% FDR cutoff using XiFDR (v., ()). Along with the 910 cross-linked PSMs, we extracted 4,161 linear PSMs from the cross-linking acquisitions as a reference data set for linear peptides. Detailed information abou […]


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xiFDR institution(s)
Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK; Chair of Bioanalytics, Institute of Biotechnology, Technische Universitat Berlin, Berlin, Germany
xiFDR funding source(s)
Supported by The Wellcome Trust through a Senior Research Fellowship (103139), a Centre Core Grant (092076), and an Instrument Grant (108504).

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