ArticleMolecular & cellular proteomics : MCP2012
TraML--a standard format for exchange of selected reaction monitoring transition lists.
Article in Molecular & cellular proteomics : MCP, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work.Journal of proteome research · 2023Review
- Cerebrospinal fluid proteome maps detect pathogen-specific host response patterns in meningitis.eLife · 2021Article
- Proteomics Standards Initiative Extended FASTA Format.Journal of proteome research · 2019Article
- Challenges and Opportunities for Biological Mass Spectrometry Core Facilities in the Developing World.Journal of biomolecular techniques : JBT · 2018Article
- Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.Journal of proteome research · 2017Article
- A multicenter study benchmarks software tools for label-free proteome quantification.Nature biotechnology · 2016Article
- Exploring the potential of public proteomics data.Proteomics · 2016Review
- Representation of selected-reaction monitoring data in the mzQuantML data standard.Proteomics · 2015Article
- Development of data representation standards by the human proteome organization proteomics standards initiative.Journal of the American Medical Informatics Association : JAMIA · 2015Review
- Making proteomics data accessible and reusable: current state of proteomics databases and repositories.Proteomics · 2015Review
- Building high-quality assay libraries for targeted analysis of SWATH MS data.Nature protocols · 2015Article
- Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry.Molecular & cellular proteomics : MCP · 2015Article
- qcML: an exchange format for quality control metrics from mass spectrometry experiments.Molecular & cellular proteomics : MCP · 2014Article
- jmzTab: a java interface to the mzTab data standard.Proteomics · 2014Article
- The jmzQuantML programming interface and validator for the mzQuantML data standard.Proteomics · 2014Article
- Differential expression of serum/plasma proteins in various infectious diseases: specific or nonspecific signatures.Proteomics. Clinical applications · 2014Review
- Controlled vocabularies and ontologies in proteomics: overview, principles and practice.Biochimica et biophysica acta · 2014Review
- A tutorial for software development in quantitative proteomics using PSI standard formats.Biochimica et biophysica acta · 2014Review
- Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.Biochimica et biophysica acta · 2014Review
- The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics.Molecular & cellular proteomics : MCP · 2013Article
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Authors and funding
14 authors.
Funding
Abstract
Targeted proteomics via selected reaction monitoring is a powerful mass spectrometric technique affording higher dynamic range, increased specificity and lower limits of detection than other shotgun mass spectrometry methods when applied to proteome analyses. However, it involves selective measurement of predetermined analytes, which requires more preparation in the form of selecting appropriate signatures for the proteins and peptides that are to be targeted. There is a growing number of software programs and resources for selecting optimal transitions and the instrument settings used for the detection and quantification of the targeted peptides, but the exchange of this information is hindered by a lack of a standard format. We have developed a new standardized format, called TraML, for encoding transition lists and associated metadata. In addition to introducing the TraML format, we demonstrate several implementations across the community, and provide semantic validators, extensive documentation, and multiple example instances to demonstrate correctly written documents. Widespread use of TraML will facilitate the exchange of transitions, reduce time spent handling incompatible list formats, increase the reusability of previously optimized transitions, and thus accelerate the widespread adoption of targeted proteomics via selected reaction monitoring.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.