ArticleMolecular & cellular proteomics : MCP2013
The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics.
Article in Molecular & cellular proteomics : MCP, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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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
32 citing papers in PubMed.
- Tidyproteomics: an open-source R package and data object for quantitative proteomics post analysis and visualization.BMC bioinformatics · 2023Article
- Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work.Journal of proteome research · 2023Review
- A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics.Metabolites · 2022Review
- Software Options for the Analysis of MS-Proteomic Data.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Article
- Proteomics Standards Initiative Extended FASTA Format.Journal of proteome research · 2019Article
- iProX: an integrated proteome resource.Nucleic acids research · 2019Article
- The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.Genome biology · 2018Article
- Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.Journal of proteome research · 2017Article
- Algorithms and design strategies towards automated glycoproteomics analysis.Mass spectrometry reviews · 2017Review
- The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.Molecular & cellular proteomics : MCP · 2017Article
- A Golden Age for Working with Public Proteomics Data.Trends in biochemical sciences · 2017Review
- CSF-PR 2.0: An Interactive Literature Guide to Quantitative Cerebrospinal Fluid Mass Spectrometry Data from Neurodegenerative Disorders.Molecular & cellular proteomics : MCP · 2017Article
- Public proteomics data: How the field has evolved from sceptical inquiry to the promise ofEuPA open proteomics · 2016Article
- 2016 update of the PRIDE database and its related tools.Nucleic acids research · 2016Article
- Exploring the potential of public proteomics data.Proteomics · 2016Review
- The mzqLibrary--An open source Java library supporting the HUPO-PSI quantitative proteomics standard.Proteomics · 2015Article
- Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics.Proteomics. Clinical applications · 2015Review
- 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
Corrections and comments
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Authors and funding
16 authors.
Funding
Abstract
The range of heterogeneous approaches available for quantifying protein abundance via mass spectrometry (MS)(1) leads to considerable challenges in modeling, archiving, exchanging, or submitting experimental data sets as supplemental material to journals. To date, there has been no widely accepted format for capturing the evidence trail of how quantitative analysis has been performed by software, for transferring data between software packages, or for submitting to public databases. In the context of the Proteomics Standards Initiative, we have developed the mzQuantML data standard. The standard can represent quantitative data about regions in two-dimensional retention time versus mass/charge space (called features), peptides, and proteins and protein groups (where there is ambiguity regarding peptide-to-protein inference), and it offers limited support for small molecule (metabolomic) data. The format has structures for representing replicate MS runs, grouping of replicates (for example, as study variables), and capturing the parameters used by software packages to arrive at these values. The format has the capability to reference other standards such as mzML and mzIdentML, and thus the evidence trail for the MS workflow as a whole can now be described. Several software implementations are available, and we encourage other bioinformatics groups to use mzQuantML as an input, internal, or output format for quantitative software and for structuring local repositories. All project resources are available in the public domain from the HUPO Proteomics Standards Initiative http://www.psidev.info/mzquantml.
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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.