ArticleProteomics2014
A standardized framing for reporting protein identifications in mzIdentML 1.2.
Article in Proteomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed, 24 citations in OpenAlex.
- Improved Protein Identification in Shotgun Proteomics with a Group-Level Extension of the LPGF Model.Journal of proteome research · 2026Article
- Quality Control in the Mass Spectrometry Proteomics Core: A Practical Primer.Journal of biomolecular techniques : JBT · 2024Article
- Computational approaches to identify sites of phosphorylation.Proteomics · 2024Review
- Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases.Briefings in bioinformatics · 2021Article
- CIDer: A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation.Journal of proteome research · 2021Article
- Interactive Peptide Spectral Annotator: A Versatile Web-based Tool for Proteomic Applications.Molecular & cellular proteomics : MCP · 2019Article
- The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.Molecular & cellular proteomics : MCP · 2017Article
- A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline.Journal of proteome research · 2016Article
- Characterisation of the circulating acellular proteome of healthy sheep using LC-MS/MS-based proteomics analysis of serum.Proteome science · 2016Article
- The SEQUEST family tree.Journal of the American Society for Mass Spectrometry · 2015Article
- Development of data representation standards by the human proteome organization proteomics standards initiative.Journal of the American Medical Informatics Association : JAMIA · 2015Review
- Review
Corrections and comments
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Authors and funding
14 authors at 12 institutions in 5 countries.
Funding
Abstract
Inferring which protein species have been detected in bottom-up proteomics experiments has been a challenging problem for which solutions have been maturing over the past decade. While many inference approaches now function well in isolation, comparing and reconciling the results generated across different tools remains difficult. It presently stands as one of the greatest barriers in collaborative efforts such as the Human Proteome Project and public repositories such as the PRoteomics IDEntifications (PRIDE) database. Here we present a framework for reporting protein identifications that seeks to improve capabilities for comparing results generated by different inference tools. This framework standardizes the terminology for describing protein identification results, associated with the HUPO-Proteomics Standards Initiative (PSI) mzIdentML standard, while still allowing for differing methodologies to reach that final state. It is proposed that developers of software for reporting identification results will adopt this terminology in their outputs. While the new terminology does not require any changes to the core mzIdentML model, it represents a significant change in practice, and, as such, the rules will be released via a new version of the mzIdentML specification (version 1.2) so that consumers of files are able to determine whether the new guidelines have been adopted by export software.
Indexed as
Identifiers
What OpenQuestion holds
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.