ReviewProteomics2015
Making proteomics data accessible and reusable: current state of proteomics databases and repositories.
Review in Proteomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
88 citing papers in PubMed.
- usiGrabber: automating the curation of proteomics spectra data at scale, making large datasets ready for use in machine learning systems.Bioinformatics (Oxford, England) · 2026Article
- Fertility Management in Pollinators: Queen Storage, Transport, and Reproductive Resilience inInsects · 2026Review
- Machine Learning-Assisted Plasma Metabolomics Identifies a Five-Metabolite Panel for Colorectal Cancer Detection.ACS omega · 2026Article
- Review
- PaxDb v6.0: reprocessed, LLM-selected, curated protein abundance data across organisms.Nucleic acids research · 2026Article
- Profiler: an open web platform for multi-omics analysis.Bioinformatics (Oxford, England) · 2026Article
- Multi-omics in cardiac arrest: a systematic review.Resuscitation plus · 2026Review
- Article
- Assessing Milk Authenticity Using Protein and Peptide Biomarkers: A Decade of Progress in Species Differentiation and Fraud Detection.Foods (Basel, Switzerland) · 2025Review
- Integrated data-driven biotechnology research environments.Database : the journal of biological databases and curation · 2025Review
- The PRIDE database at 20 years: 2025 update.Nucleic acids research · 2025Article
- Challenges and opportunities in sharing microbiome data and analyses.Nature microbiology · 2023Review
- Carotenoids in Health as Studied by Omics-Related Endpoints.Advances in nutrition (Bethesda, Md.) · 2023Review
- Spectroscape enables real-time query and visualization of a spectral archive in proteomics.Nature communications · 2023Article
- Mass spectrometry-based retina proteomics.Mass spectrometry reviews · 2023Review
- Discovery and characterization of a new class of O-linking oligosaccharyltransferases from the Moraxellaceae family.Glycobiology · 2023Article
- Grad-seq analysis ofmicroLife · 2023Article
- Variability analysis of LC-MS experimental factors and their impact on machine learning.GigaScience · 2022Article
- Pathway Analysis for Cancer Research and Precision Oncology Applications.Advances in experimental medicine and biology · 2022Article
- A proteomics sample metadata representation for multiomics integration and big data analysis.Nature communications · 2021Review
28 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
5 authors.
Funding
Abstract
Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data.
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.