ArticleMolecular & cellular proteomics : MCP2012
The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.
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 65 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
65 citing papers in PubMed.
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- The boundary of life and death: changes in mitochondrial and cytosolic proteomes associated with programmed cell death ofFrontiers in plant science · 2023Article
- Exposure to theMicrobiology (Reading, England) · 2022Article
- The effect of temperature conditioning (9°C and 20°C) on the proteome of entomopathogenic nematode infective juveniles.PloS one · 2022Article
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- From chemoproteomic-detected amino acids to genomic coordinates: insights into precise multi-omic data integration.Molecular systems biology · 2021Article
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- Proteomic analysis of the processes leading to Madurella mycetomatis grain formation in Galleria mellonella larvae.PLoS neglected tropical diseases · 2020Article
- Exposure ofJournal of fungi (Basel, Switzerland) · 2020Article
- The Impacts of Sortase A and the 4'-Phosphopantetheinyl Transferase Homolog Sfp onFrontiers in microbiology · 2020Article
- Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause.BMC genomics · 2019Article
- Citrulline Effect Is a Characteristic Feature of Deiminated Peptides in Tandem Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2019Article
- The liver proteome in a mouse model for Ascaris suum resistance and susceptibility: evidence for an altered innate immune response.Parasites & vectors · 2019Article
- Proteomic Analysis of the Responses ofJournal of fungi (Basel, Switzerland) · 2019Article
- iProX: an integrated proteome resource.Nucleic acids research · 2019Article
- The Human Cathelicidin Antimicrobial Peptide LL-37 Promotes the Growth of the Pulmonary Pathogen Aspergillus fumigatus.Infection and immunity · 2018Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors.
Funding
Abstract
The original PRIDE Converter tool greatly simplified the process of submitting mass spectrometry (MS)-based proteomics data to the PRIDE database. However, after much user feedback, it was noted that the tool had some limitations and could not handle several user requirements that were now becoming commonplace. This prompted us to design and implement a whole new suite of tools that would build on the successes of the original PRIDE Converter and allow users to generate submission-ready, well-annotated PRIDE XML files. The PRIDE Converter 2 tool suite allows users to convert search result files into PRIDE XML (the format needed for performing submissions to the PRIDE database), generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra, or by merging several PRIDE XML files together. All the tools have both a graphical user interface that provides a dialog-based, user-friendly way to convert and prepare files for submission, as well as a command-line interface that can be used to integrate the tools into existing or novel pipelines, for batch processing and power users. The PRIDE Converter 2 tool suite will thus become a cornerstone in the submission process to PRIDE and, by extension, to the ProteomeXchange consortium of MS-proteomics data repositories.
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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.