xiFDR protocols

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xiFDR specifications

Information


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

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Maintainer


  • person_outline Juri Rappsilber <>

Additional information


http://xi3.bio.ed.ac.uk/downloads/xiFDR/

Publication for xiFDR

xiFDR in pipeline

2017
PMCID: 5527848
PMID: 28743795
DOI: 10.15252/msb.20167412

[…] 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., for each protein pair, interactions based on structural homologs were predicted using mechismo (betts et al, ), saccharomyces cerevisiae orthologs […]


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xiFDR in publications

 (5)
PMCID: 5527848
PMID: 28743795
DOI: 10.15252/msb.20167412

[…] 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., for each protein pair, interactions based on structural homologs were predicted using mechismo (betts et al, ), saccharomyces cerevisiae orthologs […]

PMCID: 5436099
PMID: 28402676
DOI: 10.1021/acs.analchem.6b04935

[…] 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 […]

PMCID: 5354267
PMID: 28317030
DOI: 10.21956/wellcomeopenres.10823.r18753

[…] 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 ., […]

PMCID: 5047652
PMID: 27454319
DOI: 10.1021/acs.analchem.6b02082

[…] 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. 1.0.6.14) 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 […]

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

[…] 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. 1.0.4.13, ()). 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 […]


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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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