Phenyx protocols

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Phenyx specifications

Information


Unique identifier OMICS_02473
Name Phenyx
Software type Package/Module
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux
License Commercial
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Phenyx

Phenyx in pipeline

2017
PMCID: 5461543
PMID: 28336725
DOI: 10.1074/mcp.M116.065078

[…] identification and quantification as previously described (). peaklist files were searched against the uniprot human reference proteome (release 09/01/2013, containing 87,613 entries) using phenyx® (version 2.6.1, genebio) () with a precursor ion tolerance of 10 parts per million and a fragment ion tolerance of 0.6 da. variable peptide modifications included tmt-modified n termini […]


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Phenyx in publications

 (13)
PMCID: 5738113
PMID: 29261807
DOI: 10.1371/journal.ppat.1006758

[…] using proteowizard software v2.1.2708 [] and searched against the human swissprot protein database (v. 2013.01) using the two search engines, mascot (v2.3.02, matrixscience, london, uk) [] and phenyx (v2.6, genebio, geneva, switzerland) []. the search parameters were set with carbamidomethyl cysteine and oxidized methionine as fixed and variable modifications, respectively. one missed […]

PMCID: 5836375
PMID: 29208752
DOI: 10.1074/mcp.RA117.000186

[…] against the human swissprot database version v2016.11 (37,398 sequences, including isoforms as obtained from varsplic.pl) with the search engines mascot (v2.3.02, matrixscience, london, u.k.) and phenyx (v2.5.14, genebio, geneva, switzerland) (). submission to the search engines was done via a perl script that performs an initial search with relatively broad mass tolerances (mascot only) […]

PMCID: 5236063
PMID: 27916275
DOI: 10.1016/j.cell.2016.11.010

[…] database v2013.01_20130110 (24,615 sequences including isoforms obtained from varsplic.pl () and appended known contaminants) with the search engines mascot (v2.2.03, matrixscience, london, uk) and phenyx (v2.5.14, genebio, geneva, switzerland) (). submission to the search engines was via a perl script that performs an initial search with relatively broad mass tolerances (mascot only) […]

PMCID: 4813694
PMID: 26933192
DOI: 10.1074/mcp.O115.055350

[…] and 24,830 sequences, respectively, including isoforms obtained from varsplic.pl () and appended with known contaminants) with the search engines mascot (v2.3.02, matrixscience, london, uk) and phenyx (v2.5.14, genebio, geneva, switzerland) (). submission to the search engines was via a perl script that performs an initial search with relatively broad mass tolerances (mascot only) […]

PMCID: 4376665
PMID: 25561175
DOI: 10.1038/nature14107

[…] and searched against human swissprot database version v2013.01_20130110 (37,261 sequences and common contaminants). the search engines mascot (v2.3.02, matrixscience, london, uk) and phenyx (v2.5.14, genebio, geneva, switzerland) were used. the searches were submitted to mascot using in-house perl scripts at precursor and fragment ions mass tolerances ±10 ppm and ± 0.6 da, […]


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Phenyx institution(s)
GeneProt Inc, Meyrin, Switzerland

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