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TIQAM specifications

Information


Unique identifier OMICS_03330
Name TIQAM
Alternative name Targeted Identification for Quantitative Analysis by MRM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Targeted Identification for Quantitative Analysis by MRM

TIQAM citations

 (8)
library_books

Making proteomics data accessible and reusable: Current state of proteomics databases and repositories

2015
Proteomics
PMCID: 4409848
PMID: 25158685
DOI: 10.1002/pmic.201400302

[…] omics workflows in different ways: (i) SRMAtlas (http://www.srmatlas.org/) is a compendium of targeted proteomics assays to detect and quantify proteins using SRM/MRM-based proteomics workflows; (ii) TIQAM (targeted identification for quantitative analysis by MRM) [], which is a desktop application to facilitate the selection of peptide and transitions. It consists of three applications: “TIQAM-Di […]

library_books

Modeling and systematic analysis of biomarker validation using selected reaction monitoring

2014
EURASIP J Bioinform Syst Biol
PMCID: 5270363
PMID: 28194167
DOI: 10.1186/s13637-014-0017-y

[…] d upon the experiments on the QQQ instrument or data from previously done shotgun experiments, two to four fragment ions are selected for each PTP. For example, being integrated with PeptideAtlas [], TIQAM [] can be used in this step [].Determination of the pairs of m/z values for the first and third quadrupoles is referred to as the selection of a transition[]. The selection of transitions are of […]

library_books

The role of quantitative mass spectrometry in the discovery of pancreatic cancer biomarkers for translational science

2014
J Transl Med
PMCID: 3998064
PMID: 24708694
DOI: 10.1186/1479-5876-12-87

[…] ta. The dedicated analysis software “Skyline”, supports the direct picking of peptide, precursor and transition in silico from proteins and fragment peptides []. Other platform-specific tools include TIQAM, MRMPilot, SRM Workflow Software, Verify, and Optimizer []. MRMer is another open source software tool, for the analysis of data generated by highly complex MRM-MS experiments. It provides a rap […]

library_books

Integrative Toxicoproteomics Implicates Impaired Mitochondrial Glutathione Import as an Off Target Effect of Troglitazone

2013
J Proteome Res
PMCID: 3805328
PMID: 23659346
DOI: 10.1021/pr400219s

[…] arameters were optimized at an ion spray voltage of 2800 V, with ion source gas 1 at 40 V, and with the interface heater temperature at 150 °C. The MRM transitions of the peptides were generated from TIQAM software (www.proteomecenter.org). Peptides were excluded where there were cysteines and methionines and peptides with two and more consecutive basic amino acids on either the C- or N-terminus. […]

library_books

TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists*

2011
PMCID: 3322582
PMID: 22159873
DOI: 10.1074/mcp.R111.015040

[…] SSEL, and QuAD that provide recommended transitions based on user input; the many existing transitions lists that are already in common use; SRM experiment design and analysis software such as ATAQS, TIQAM, Skyline, and others; and the instruments themselves via their control software. If all or most of these tools can exchange annotated transition lists in a common format, the hassle of transform […]

library_books

Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further research

2010
J Proteomics
PMCID: 2958306
PMID: 20615486
DOI: 10.1016/j.jprot.2010.06.008

[…] eomics assays to detect and quantify yeast proteins in complex proteome digests by mass spectrometry . It currently contains assays for nearly 1500 S. cerevisiae proteins (21% of the yeast proteome).-TIQAM (Targeted Identification for Quantitative Analysis by MRM) , a desktop Java application to facilitate the selection of peptide and transitions. It consists of three applications: TIQAM-Digestor, […]

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