xiFDR statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool xiFDR
info

Tool usage distribution map

This map represents all the scientific publications referring to xiFDR per scientific context
info info

Associated diseases

info

Popular tool citations

chevron_left Database search chevron_right
Want to access the full stats & trends on this tool?

Protocols

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

Download


download.png

Versioning


No version available

Maintainer


  • person_outline Juri Rappsilber

Additional information


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

Publication for xiFDR

xiFDR citations

 (5)
library_books

Capturing protein communities by structural proteomics in a thermophilic eukaryote

2017
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. […]

call_split

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

2017
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 […]

call_split

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

2016
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 . […]

call_split

Optimized Fragmentation Regime for Diazirine Photo Cross Linked Peptides

2016
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. 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 (Unipro […]

call_split

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

2015
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. 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 abou […]


Want to access the full list of citations?
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).

xiFDR reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review xiFDR