X! Tandem protocols

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X! Tandem specifications

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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

 (14)
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 [] version 4.3. peptide/protein identifications were validated by peptide/proteinprophet [, ]., de-identified […]

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). each raw data file was first converted to mzxml using the msconvert tool incorporated in proteowizard (version […]

2015
PMCID: 4518706
PMID: 26220445
DOI: 10.1186/s12864-015-1768-x

[…] data was obtained in raw format and converted to the mzxml [] format, using msconvert [] with centroiding of ms1 and ms2 data, and deisotoping of ms2 data. for spectrum to sequence assignment x! tandem (version 2013.09.01) [] was used. the proteome database consisted of human reviewed canonical uniprot sequences (without isoforms, 20,240 protein entries) downloaded from uniprot […]

2015
PMCID: 4687979
PMID: 26715830
DOI: 10.4137/CIN.S35374

[…] against version 3.44 of the human international protein index (ipi) (71,884 protein entries) and mouse ipi (version 3.44 with 55,078 protein entries) databases. the searches were performed with x! tandem (version 2008.02.01). the mass tolerance for precursor ions was set to 5 ppm. the mass tolerance for fragment ions was set to 0.5 da. a fixed modification of 71.0371 mass units was added […]

2015
PMCID: 4687979
PMID: 26715830
DOI: 10.4137/CIN.S35374

[…] sequences in human database (human ipi version 3.44) and mouse database (mouse ipi version 3.44) were computationally digested with trypsin, and a minimum of seven residues was used to match the x! tandem default search parameter of the minimum parent fragment., to facilitate comparisons of protein groups among samples, data were aligned by tracking all proteins that were members of a single […]


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X! Tandem in publications

 (243)
PMCID: 5940405
PMID: 29765546
DOI: 10.18632/oncotarget.25106

[…] into a capillary hplc system coupled to a mass spectrometer via a nanospray ionization source (es ms/ms). all ms/ms samples were analyzed using mascot (matrix science, london, uk; version 2.4.1) and x! tandem softwares. mascot was set up to search the tax_homosapiens_9606_20141128 database. x! tandem was set up to search a subset of the tax_homosapiens_9606_20141128 database. for protein […]

PMCID: 5912190
PMID: 29696078
DOI: 10.1080/20013078.2018.1456888

[…] raw ms/ms files after they were converted to mzxml using msconvert. the mzxml files were searched against the swiss-prot reviewed human fasta database (33,330 proteins and decoys) using the comet, x! tandem native and x! tandem k-score search algorithms [,]. target-decoy modelling of peptide spectral matches was performed with peptide prophet [] using the following criteria: fragment […]

PMCID: 5847575
PMID: 29531254
DOI: 10.1038/s41598-018-22610-4

[…] pseudo-ms/ms correlative precursor-fragment feature extraction using dia-umpire. the spectral libraries were generated following a previously optimized procedure at <1% fdr using a combination of x! tandem and comet search engines. the libraries were used to quantify peptides in an unfractionated, whole-cell saccharomyces cerevisiae tryptic digest, of which 10 µg were separated on 60 min […]

PMCID: 5877945
PMID: 29463717
DOI: 10.1073/pnas.1716925115

[…] purified myosin from four or five hearts per group were digested with trypsin and then reduced and alkylated. digested peptides were analyzed by ms, and protein identification was determined using x! tandem (). relative amounts of human versus mouse protein were determined by the ratio of the number of human-specific peptides (aggansn or eevdqm) or mouse-specific peptides (ieggssn or eeidqm) […]

PMCID: 5801471
PMID: 29437928
DOI: 10.1128/mBio.02394-17

[…] 89.0% probability to achieve an fdr of less than 1.0%. peptide probabilities evaluated using sequest software were assigned by the scaffold local fdr algorithm. peptide probabilities evaluated using x! tandem software were assigned by the peptide prophet algorithm () with scaffold delta-mass correction. protein identifications were accepted if they could be established to achieve an fdr of less […]


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

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