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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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No version available

Publication for X! Tandem

X! Tandem citations

 (281)
library_books

Proteomic screening identifies the zonula occludens protein ZO 1 as a new partner for ADAM12 in invadopodia like structures

2018
Oncotarget
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 identifi […]

library_books

Newt cells secrete extracellular vesicles with therapeutic bioactivity in mammalian cardiomyocytes

2018
J Extracell Vesicles
PMCID: 5912190
PMID: 29696078
DOI: 10.1080/20013078.2018.1456888

[…] he 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 tolerance: […]

library_books

Cost effective generation of precise label free quantitative proteomes in high throughput by microLC and data independent acquisition

2018
Sci Rep
PMCID: 5847575
PMID: 29531254
DOI: 10.1038/s41598-018-22610-4

[…] by 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 micro […]

library_books

Sarcomeric perturbations of myosin motors lead to dilated cardiomyopathy in genetically modified MYL2 mice

2018
Proc Natl Acad Sci U S A
PMCID: 5877945
PMID: 29463717
DOI: 10.1073/pnas.1716925115

[…] se 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) fo […]

call_split

Exploring the Antimicrobial Action of Quaternary Amines against Acinetobacter baumannii

2018
MBio
PMCID: 5801471
PMID: 29437928
DOI: 10.1128/mBio.02394-17
call_split See protocol

[…] 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 t […]

call_split

Decellularization and Solubilization of Porcine Liver for Use as a Substrate for Porcine Hepatocyte Culture

2018
PMCID: 5802637
PMID: 29390876
DOI: 10.1177/0963689717742157
call_split See protocol

[…] d as variable modifications; trypsin was specified as the proteolytic enzyme, with 1 missed cleavage allowed. The Mascot results files were combined for subset searching of the identified proteins by X! Tandem cross-correlation with the Mascot results, and determination of protein and peptide identity probabilities was accomplished by Scaffold (Proteome Software, Inc., Portland, OR, USA). The thre […]

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

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