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Protocols

Crux specifications

Information


Unique identifier OMICS_02401
Name Crux
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline William Noble

Publications for Crux

Crux citations

 (19)
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A large scale Plasmodium vivax Saimiri boliviensis trophozoite schizont transition proteome

2017
PLoS One
PMCID: 5567661
PMID: 28829774
DOI: 10.1371/journal.pone.0182561
call_split See protocol

[…] alyzed, one using only carbamidomethyl-cys and met sulfoxide as variable modifications, the second using a more extensive set of oxidative modifications (below). The fourth search engine utilized was Crux with Percolator scoring []; proteins were accepted to a maximal protein q value of 0.02. The fifth search engine was MSGF Plus [], using Mascot to convert Thermo.raw files to mgf format, and Prot […]

library_books

N terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana *

2017
PMCID: 5461538
PMID: 28432195
DOI: 10.1074/mcp.M116.066662

[…] causing an increase of the peptide search space (supplemental Fig. S3). To increase the number of identified Nt-peptides, all MS/MS data were searched in parallel with three search engines: COMET (), Crux () and MS-GF+ (). Results from individual searches were aggregated by calculating the combined FDR score as described by Jones et al. ().Peptides reported by individual and multiple search engine […]

library_books

TB IRIS: Proteomic analysis of in vitro PBMC responses to Mycobacterium tuberculosis and response modulation by dexamethasone

2017
PMCID: 5446321
PMID: 28209523
DOI: 10.1016/j.yexmp.2017.02.008

[…] The .RAW data files were converted to mzXML format using the Trans-Proteomic Pipeline (). Crux-Barista (version 1.37 (, )) software mapped MS/MS fragmentation spectra to a UniProtKB Human Reference Proteome FASTA file () to identify peptide-spectrum matches (PSMs). Search parameters includ […]

call_split

Using the entrapment sequence method as a standard to evaluate key steps of proteomics data analysis process

2017
BMC Genomics
PMCID: 5374549
PMID: 28361671
DOI: 10.1186/s12864-017-3491-2
call_split See protocol

[…] ot results for each PSM: BuildSummary’s ExpectValue, PeptideProphet’s probability, FDRAnalysis’s FDRScore and PepDistiller’s q-value. Comet and Tide results were processed by Percolator integrated in Crux, which gave a rescore of q-value. MS-GF+ and X!Tandem results were processed by percolator-converters (v3-00) followed by percolator (v2-08) for further quality control. The percolator tools can […]

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Fast and Accurate Protein False Discovery Rates on Large Scale Proteomics Data Sets with Percolator 3.0

2016
J Am Soc Mass Spectrom
PMCID: 5059416
PMID: 27572102
DOI: 10.1007/s13361-016-1460-7
call_split See protocol

[…] lues. Next, we assigned high-resolution precursor masses and charges using information from the precursor scans with Hardklör [] followed by Bullseye [], both with the default parameters, through the Crux 2.0 package interface [].For the Kim data set, the data was searched against the human Swiss-Prot and Swiss-Prot+TrEMBL databases (http://www.uniprot.org/, accessed: November 12, 2015) concatenat […]

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Identification of Quantitative Proteomic Differences between Mycobacterium tuberculosis Lineages with Altered Virulence

2016
Front Microbiol
PMCID: 4885829
PMID: 27303394
DOI: 10.3389/fmicb.2016.00813
call_split See protocol

[…] Raw data was captured from the mass spectrometer and converted to MS2 files using MakeMS2 software (Thermo Scientific). The data was then analyzed using Crux (McIlwain et al., ) and Mascot (Cottrell and London, ), and the output of MS2PIP (Degroeve and Martens, ) was used additional features for the Percolator algorithm. Spectra were obtained from eac […]

Citations

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Crux institution(s)
Department of Genome Sciences, University of Washington, Washington, Seattle, WA, USA; Department of Computer Science and Engineering, University of Washington, Washington, Seattle, WA, USA
Crux funding source(s)
Supported by NIH awards R01 GM121818 and P41 GM103533.

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