Research map: The need for standardization and improved open (meta)data practices in metaproteomics

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Papers in this map

  1. Prokka: rapid prokaryotic genome annotation · Torsten Seemann · 2014 · 20457 citations · Cited by this paper
  2. maniFasta and the AllOralsDB: simplifying construction of comprehensive reference databases for metaproteomics · Christopher R. Handelmann · 2026 · Cites this paper
  3. Comprehensive analyses of archaeal viral genomes reveal genomic characteristics, divergence, and host interactions · 2026 · Related
  4. The FAIR Guiding Principles for scientific data management and stewardship · Mark D. Wilkinson · 2016 · 18951 citations · Cited by this paper
  5. Integrating multi-omics technologies to decipher microbiome functions · Tim Van Den Bossche · 2026 · Cites this paper
  6. Metabolic host-microbe crosstalk in stabilization of epithelial HIF · 2026 · Related
  7. InterProScan: protein domains identifier · Emmanuel Quévillon · 2005 · 3214 citations · Cited by this paper
  8. Gardnerella piotii enhances uropathogenic Escherichia coli infection through a succinate–GPR91–uroplakin axis · 2026 · Related
  9. The PRIDE database at 20 years: 2025 update · Yasset Pérez‐Riverol · 2024 · 2054 citations · Cited by this paper
  10. Environmental reservoirs and transmission pathways of antimicrobial resistance across the pork production continuum · 2026 · Related
  11. DRAM for distilling microbial metabolism to automate the curation of microbiome function · Michael John Shaffer · 2020 · 1252 citations · Cited by this paper
  12. Helotiales fungi as potential nutritional partners for non-mycorrhizal plants: a machine learning and experimental approach · 2026 · Related
  13. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications · Pelin Yilmaz · 2011 · 835 citations · Cited by this paper
  14. Dismissing-then-recruiting: a unique mechanism for symbiont recruitment and lignocellulose degradation in gut of black soldier fly larvae · 2026 · Related
  15. mzML—a Community Standard for Mass Spectrometry Data · Lennart Martens · 2010 · 805 citations · Cited by this paper
  16. The impact of western versus agrarian diet consumption on gut microbiome composition and immune dysfunction in people living with HIV in rural and urban Zimbabwe · 2026 · Related
  17. The minimum information about a proteomics experiment (MIAPE) · Chris F. Taylor · 2007 · 783 citations · Cited by this paper
  18. Context-dependent effects of antimicrobial coatings on microbial load and bacterial community composition on public high-touch surfaces · 2026 · Related
  19. Reporting guidelines for human microbiome research: the STORMS checklist · Chloe A. Mirzayi · 2021 · 541 citations · Cited by this paper
  20. Reconstructing community dynamics from limited observations · 2026 · Related
  21. eggNOG 6.0: enabling comparative genomics across 12 535 organisms · Ana Hernández-Plaza · 2022 · 378 citations · Cited by this paper
  22. Uncovering transcriptional processes in microbial communities adapted to differing saline conditions in salt-weathered historic buildings · 2026 · Related
  23. Quality assurance and quality control reporting in untargeted metabolic phenotyping: mQACC recommendations for analytical quality management · Jennifer Kirwan · 2022 · 210 citations · Cited by this paper
  24. A proteomics sample metadata representation for multiomics integration and big data analysis · Chengxin Dai · 2021 · 140 citations · Cited by this paper
  25. Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows · Tim Van Den Bossche · 2021 · 132 citations · Cited by this paper
  26. Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis · Henning Schiebenhoefer · 2019 · 123 citations · Cited by this paper
  27. Universal Spectrum Identifier for mass spectra · Eric W. Deutsch · 2021 · 110 citations · Cited by this paper
  28. The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes · Tim Van Den Bossche · 2021 · 109 citations · Cited by this paper
  29. The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary · Gerhard Mayer · 2013 · 105 citations · Cited by this paper
  30. Perspective and Guidelines for Metaproteomics in Microbiome Studies · Xu Zhang · 2019 · 105 citations · Cited by this paper
  31. Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing · Mak A. Saito · 2019 · 104 citations · Cited by this paper
  32. A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane · Henning Schiebenhoefer · 2020 · 95 citations · Cited by this paper
  33. The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics · Juan Antonio Vizcaíno · 2017 · 75 citations · Cited by this paper
  34. The microbiologist's guide to metaproteomics · Tim Van Den Bossche · 2025 · 73 citations · Cited by this paper
  35. BioSamples database: FAIRer samples metadata to accelerate research data management · Mélanie Courtot · 2021 · 71 citations · Cited by this paper
  36. Challenges and opportunities in sharing microbiome data and analyses · Curtis Huttenhower · 2023 · 71 citations · Cited by this paper
  37. Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work · Eric W. Deutsch · 2023 · 62 citations · Cited by this paper
  38. The lipidomics reporting checklist a framework for transparency of lipidomic experiments and repurposing resource data · Dominik Kopczynski · 2024 · 59 citations · Cited by this paper
  39. lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation · Tine Claeys · 2023 · 57 citations · Cited by this paper

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