X! Tandem protocols

X! Tandem specifications

Information


Unique identifier OMICS_02400
Name X! Tandem
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License Artistic License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for X! Tandem

X! Tandem IN pipelines

 (7)
2017
PMCID: 5755722
PMID: 29321818
DOI: 10.18632/genesandcancer.159

[…] thermo fisher ltq orbitrap velos mass spectrometer. the xcalibur raw files were converted to mzxml format using readw and were searched against the uniprotkb/swiss-prot human protein database using x! tandem. the x! tandem search results were analyzed by the trans- proteomic pipeline [33] version 4.3. peptide/protein identifications were validated by peptide/proteinprophet [34, 35]., […]

2017
PMCID: 5755722
PMID: 29321818
DOI: 10.18632/genesandcancer.159

[…] ltq orbitrap velos mass spectrometer. the xcalibur raw files were converted to mzxml format using readw and were searched against the uniprotkb/swiss-prot human protein database using x! tandem. the x! tandem search results were analyzed by the trans- proteomic pipeline [33] version 4.3. peptide/protein identifications were validated by peptide/proteinprophet [34, 35]., de-identified ewing […]

2016
PMCID: 5270547
PMID: 27791479
DOI: 10.1080/15476286.2016.1249092

[…] within 20¬†ppm for 30 seconds was used after 2 repeats of ms2 for a precursor ion. ms2 were collected with 1 microscan and a collision energy of 35%., we performed peptide identification using x! tandem incorporated in a trans-proteomic pipeline (version 4.6 occupy rev 2).56 each raw data file was first converted to mzxml using the msconvert tool incorporated in proteowizard (version […]

2014
PMCID: 4123944
PMID: 24999758
DOI: 10.1021/pr500387m

[…] to mzxml format using readw (http://tools.proteomecenter.org/wiki/index.php?title=software:readw) and were searched against the ipi human protein database (v 3.24; 66,923 protein entries) using x! tandem. methionine oxidation was considered as a variable modification in all searches, and lysine biotinylation was included for the bioid experiments. up to one missed tryptic cleavage […]

2014
PMCID: 4123944
PMID: 24999758
DOI: 10.1021/pr500387m

[…] methionine oxidation was considered as a variable modification in all searches, and lysine biotinylation was included for the bioid experiments. up to one missed tryptic cleavage was allowed. the x! tandem search results were analyzed by the trans-proteomic pipeline14 version 4.3. peptide/protein identifications were validated by peptide/proteinprophet.15,16 a proteinprophet score of 0.9 […]

X! Tandem institution(s)
Manitoba Centre for Proteomics, University of Manitoba, Winnipeg, MB, Canada

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