ArticleProteomics2011
Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets.
Article in Proteomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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.
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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
14 citing papers in PubMed.
- RBC-GEM: A genome-scale metabolic model for systems biology of the human red blood cell.PLoS computational biology · 2025Article
- Last rolls of the yoyo: Assessing the human canonical protein count.F1000Research · 2017Review
- Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.Journal of proteome research · 2016Article
- Making proteomics data accessible and reusable: current state of proteomics databases and repositories.Proteomics · 2015Review
- Analysis of the tryptic search space in UniProt databases.Proteomics · 2015Article
- PhosphoSitePlus, 2014: mutations, PTMs and recalibrations.Nucleic acids research · 2015Article
- Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes.Human molecular genetics · 2014Article
- PIQMIe: a web server for semi-quantitative proteomics data management and analysis.Nucleic acids research · 2014Article
- What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins.Molecular biology of the cell · 2014Review
- Article
- A repository of assays to quantify 10,000 human proteins by SWATH-MS.Scientific data · 2014Article
- The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.Nucleic acids research · 2013Article
- Improvements in the Protein Identifier Cross-Reference service.Nucleic acids research · 2012Article
- The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection.Nucleic acids research · 2012Article
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Authors and funding
6 authors.
Funding
Abstract
The International Protein Index (IPI) database has been one of the most widely used protein databases in MS proteomics approaches. Recently, the closure of IPI in September 2011 was announced. Its recommended replacement is the new UniProt Knowledgebase (UniProtKB) "complete proteome" sets, launched in May 2011. Here, we analyze the consequences of IPI's discontinuation for human and mouse data, and the effect of its substitution with UniProtKB on two levels: (i) data already produced and (ii) newly performed experiments. To estimate the effect on existing data, we investigated how well IPI identifiers map to UniProtKB accessions. We found that 21% of human and 10% of mouse identifiers do not map to UniProtKB and would thus be "lost." To investigate the impact on new experiments, we compared the theoretical search space (i.e. the tryptic peptides) of both resources and found that it is decreased by 14.0% for human and 8.9% for mouse data through IPI's closure. An analysis on the experimental evidence for these "lost" peptides showed that the vast majority has not been identified in experiments available in the major proteomics repositories. It thus seems likely that the search space provided by UniProtKB is of higher quality than the one currently provided by IPI.
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Registered trials
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