Phenyx

[…] 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 […]

[…] 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 […]

[…] 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) […]

[…] 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) […]

[…] 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) […]

[…] 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, […]