Integrated proteogenomics database

When using the iPtgxDB web service, please cite

An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics

U. Omasits, A. R. Varadarajan, M. Schmid, S. Goetze, D. Melidis, M. Bourqui, O. Nikolayeva, M. Quebatte, A. Patrignani, C. Dehio, J. E. Frey, M. D. Robinson, B. Wollscheid, and C. H. Ahrens

Genome Research, 27 , 2083-2095, 2017

Selected publications that used/referenced the iPtgxDB solution

  1. Bartel J, et al. 2026. Less missing values — evaluation of proteomics workflows for the quantification of (small) proteins. microLife 7:uqag002. 10.1093/femsml/uqag002.
  2. Štambuk N, et al. 2025. Relational model of all genetic codes. BioSystems 257:105600. 10.1016/j.biosystems.2025.105600.
  3. Franco PHC, et al. 2025. Detection and quantitation of small proteins using mass spectrometry. Molecular & Cellular Proteomics 24:101052. 10.1016/j.mcpro.2025.101052.
  4. uz‑Zaman M and Ochman H. 2025. Propensity for proto-gene emergence in bacteria. Genome Biology 26:362. 10.1186/s13059-025-03825-x.
  5. Li J, et al. 2025. VirNucPro: an identifier for the identification of viral short sequences using six-frame translation and large language models. Briefings in Bioinformatics 26:bbaf224. 10.1093/bib/bbaf224.
  6. Kraus A and Hess WR. 2025. How small proteins adjust the metabolism of cyanobacteria under stress: the role of small proteins in cyanobacterial stress responses. BioEssays 47:e202400245. 10.1002/bies.202400245.
  7. uz-Zaman H and Ochman H. 2025. De novo gene birth and the conundrum of ORFan genes in bacteria. Genome Research 35:1679-1688. 10.1101/gr.280157.124.
  8. Jia C, et al. 2024. Salmonella phylogenomics. In: Phylogenomics 2024:267-281. 10.1016/B978-0-323-99886-4.00019-3.
  9. Bhattacharjee B, et al. 2024. Proteogenomics and immunopeptidomics in the development of advanced vaccines. In Advanced Vaccination Technologies for Infectious and Chronic Diseases 455-475. 10.1016/B978-0-443-18564-9.00019-9.
  10. Coelho LP, et al. 2024. Challenges in computational discovery of bioactive peptides in ’omics data. Proteomics. 24:2300105. 10.1002/pmic.202300105.
  11. Tufail MA, et al. 2024. Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions. Nature Communications 15:8659. 10.1038/s41467-024-53008-8.
  12. Raj A, et al. 2023. Proteogenomics 101: a primer on database search strategies. Journal of Proteins and Proteomics 14:287-301. 10.1007/s42485-023-00118-4.
  13. Dimonaco NJ, et al. 2023. StORF-Reporter: finding genes between genes. Nucleic Acids Research 51(21):11504-11517. 10.1093/nar/gkad814.
  14. Genth J, et al. 2023. Identification of proteoforms of short open reading frame-encoded peptides in Blautia producta under different cultivation conditions. Microbiology Spectrum 11:e02528-23. 10.1128/spectrum.02528-23.
  15. Fuchs S and Engelmann S. 2023. Small proteins in bacteria – Big challenges in prediction and identification. Proteomics 23:2200421. 10.1002/pmic.202200421.
  16. Meier-Credo J, et al. 2023. Detection of known and novel small proteins in Pseudomonas stutzeri Using a Combination of Bottom-Up and Digest-Free Proteomics and Proteogenomics. Analytical Chemistry 95:11892-11900. 10.1021/acs.analchem.3c00676.
  17. Hug S, et al. 2023. Paraburkholderia sabiae uses one type VI secretion system (T6SS-1) as a powerful weapon against notorious plant pathogens. Microbiology Spectrum 11:e0162223. 10.1128/spectrum.01622-23.
  18. Hadjeras L, et al. 2023. Unraveling the small proteome of the plant symbiont Sinorhizobium meliloti by ribosome profiling and proteogenomics. microLife 4:uqad012. 10.1093/femsml/uqad012.
  19. Hadjeras L, et al. 2023. Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimized mass spectrometry. microLife 4:uqad001. 10.1093/femsml/uqad001.
  20. Fijalkowski I, et al. 2022. Hidden in plain sight: challenges in proteomics detection of small ORF-encoded polypeptides. microLife 3:uqac005. 10.1093/femsml/uqac005.
  21. Aggarwal S, et al. 2022. False discovery rate: the Achilles’ heel of proteogenomics. Briefings in Bioinformatics 23:5. 10.1093/bib/bbac163.
  22. Fancello L & Burger T. 2022. An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics. Genome Biology 23:1. 10.1186/s13059-022-02701-2.
  23. Zhu H, et al. 2022. Ac-LysargiNase efficiently helps genome reannotation of Mycolicibacterium smegmatis MC2 155. Journal of Proteomics 264. 10.1016/j.jprot.2022.104622.
  24. Chen L, et al. 2022. The small open reading frame-encoded peptides: advances in methodologies and functional studies. ChemBioChem 23:e202100534. 10.1002/cbic.202100534.
  25. Escudeiro P, et al. 2022. Functional characterization of prokaryotic dark matter: the road so far and what lies ahead. Current Research in Microbial Sciences 3:100159. 10.1016/j.crmicr.2022.100159.
  26. Ahrens CH, et al. 2022. A practical guide to small protein discovery and characterization using mass spectrometry Journal of Bacteriology 204:1. 10.1128/jb.00353-21.
  27. Stringer A, et al. 2022. Identification of novel translated small open reading frames in Escherichia coli using complementary ribosome profiling approachesJournal of Bacteriology 204:1. 10.1128/JB.00352-21.
  28. Kimbrel JA, et al. 2022. Prokaryotic genome annotation. Methods in Molecular Biology 2349:193-214. 10.1007/978-1-0716-1585-0_10.
  29. He C, et al. 2021. Proteogenomics integrating novel junction peptide identification strategy discovers three novel protein isoforms of human NHSL1 and EEF1B2. Journal of Proteome Research 20:5294-5303. 10.1021/acs.jproteome.1c00373.
  30. Parmar BS, et al. 2021. Identification of non-canonical translation products in C. elegans using tandem mass spectrometry. Frontiers in Genetics 12. 10.3389/fgene.2021.728900.
  31. Fijalkowski I, et al. 2021. Small protein enrichment improves proteomics detection of sORF encoded polypeptides. Frontiers in Genetics 12. 10.3389/fgene.2021.713400.
  32. Yu S, et al. 2021. Proteogenomic analysis provides novel insight into genome annotation and nitrogen metabolism in nostoc sp. pcc 7120. Microbiology Spectrum 9:2. 10.1128/Spectrum.00490-21.
  33. Vitorino R, et al. 2021. Peptidomics and proteogenomics: background, challenges and future needs. Expert Review of Proteomics 2021. 10.1080/14789450.2021.1980388.
  34. Cassidy L, et al. 2021. Bottom-up and top-down proteomic approaches for the identification, characterization, and quantification of the low molecular weight proteome with focus on short open reading frame-encoded peptides. Proteomics 21:23-24. 10.3389/10.1002/pmic.202100008.
  35. Fuchs S, et al. 2021. Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach. PLOS Genetics 17:6. 10.1371/journal.pgen.1009585.
  36. Jorge GL, et al. 2021. Identification of novel protein-coding sequences in Eucalyptus grandis plants by high-resolution mass spectrometry. Biochimica et Biophysica Acta-Proteins and Proteomics 1869:3. 10.1016/j.bbapap.2020.140594.
  37. Petruschke H, et al. 2021. Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome. Microbiome 9:1. 10.1186/s40168-020-00981-z.
  38. Vitorino R, et al. 2021. The role of micropeptides in biology. Cellular and Molecular Life Science 78:3285-3298. 10.1007/s00018-020-03740-3.
  39. Tariq MU, et al. 2021. Methods for proteogenomics data analysis, challenges, and scalability bottlenecks: a survey. IEEE Access 9:5497-5516. 10.1109/ACCESS.2020.3047588.
  40. Varadarajan AR, et al. 2020. An integrated model system to gain mechanistic insights into biofilm formation and antimicrobial resistance development in Pseudomonas aeruginosa MPAO1. NPJ Biofilms and Microbiomes 6:1 10.1038/s41522-020-00154-8.
  41. Bartel J, et al. 2020. Optimized proteomics workflow for the detection of small proteins. Journal of Proteome Research 19:4004-4018. 10.1021/acs.jproteome.0c00286.
  42. Dahal S, et al. 2020. Synthesizing systems biology knowledge from omics using genome-scale models. Proteomics 20:1900282. 10.1002/pmic.201900282.
  43. Lutz S, et al. 2020. Harnessing the microbiomes of suppressive composts for plant protection: from metagenomes to beneficial microorganisms and reliable diagnostics. Frontiers in Microbiology 11:1810. 10.3389/fmicb.2020.01810.
  44. Reva ON, et al. 2020. Complete genome sequence and epigenetic profile of Bacillus velezensis UCMB5140 used for plant and crop protection in comparison with other plant-associated Bacillus strains. Applied Microbiology and Biotechnology 104:7643-7656. 10.1007/s00253-020-10767-w.
  45. Schulze S, et al. 2020. The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics. Nature Communications 11:1. 10.1038/s41467-020-16784-7.
  46. Melior H, et al. 2020. The leader peptide peTrpL forms antibiotic-containing ribonucleoprotein complexes for posttranscriptional regulation of multiresistance genes. MBIO 11:3. 10.1128/mBio.01027-20.
  47. De Vrieze M, et al. 2020. Linking comparative genomics of nine potato-associated Pseudomonas isolates with their differing biocontrol potential against late blight. Frontiers in Microbiology 11:857. 10.3389/fmicb.2020.00857.
  48. Varadarajan AR, et al. 2020. A proteogenomic resource enabling integrated analysis of Listeria genotype-proteotype-phenotype relationships. Journal of Proteome Research. 19:1647-1662. 10.1021/acs.jproteome.9b00842.
  49. Reva ON, et al. 2019. Genetic, epigenetic and phenotypic diversity of four Bacillus velezensis strains used for plant protection or as probiotics. Frontiers in Microbiology 10:2610. 10.3389/fmicb.2019.02610.
  50. Machado KCT, et al. 2019. On the impact of the pangenome and annotation discrepancies while building protein sequence databases for bacteria proteogenomics. Frontiers in Microbiology 10:1410. 10.3389/fmicb.2019.01410.
  51. Agrawal A, et al. 2019. Global proteome profiling reveals drug-resistant traits in Elizabethkingia meningoseptica: An opportunistic nosocomial pathogen. OMICS-A Journal of Integrative Biology 23:318-326. 10.1089/omi.2019.0039.
  52. Fernandez N, Cabrera JJ, Varadarajan AR, et al. 2019. An integrated systems approach unveils new aspects of microoxia-mediated regulation in Bradyrhizobium diazoefficiens. Frontiers in Microbiology 10:924. 10.3389/fmicb.2019.00924.
  53. Tong X & Liu S. 2019. CPPred: coding potential prediction based on the global description of RNA sequence. Nucleic Acids Research 47:e43. 10.1093/nar/gkz087.
  54. Low TY. 2019. Connecting proteomics to next-generation sequencing: proteogenomics and its current applications in biology. Proteomics 19:10 10.1002/pmic.201800235.
  55. Manes NP & Nita-Lazar A. 2018. Application of targeted mass spectrometry in bottom-up proteomics for systems biology research. Journal of Proteomics 189:75-90. 10.1016/j.jprot.2018.02.008.
  56. Yang M, et al. 2018. Genome annotation of a model diatom Phaeodactylum tricornutum using an integrated proteogenomic pipeline. Molecular Plant 11:1292-1307. 10.1016/j.molp.2018.08.005.
  57. Schmid M, et al. 2018. Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats. Nucleic Acids Research 46:8953-8965. 10.1093/nar/gky726.
  58. Lardi M & Pessi G. 2018. Functional genomics approaches to studying symbioses between legumes and nitrogen-fixing rhizobia. High Throughput 7: pii: E15. 10.3390/ht7020015.
  59. Zengerer V, et al. 2018. Pseudomonas orientalis F9: A Potent Antagonist against Phytopathogens with Phytotoxic Effect in the Apple Flower. Frontiers in Microbiology 9:145. 10.3389/fmicb.2018.00145.
  60. Schmid M, et al. 2018. Comparative genomics of completely sequenced Lactobacillus helveticus genomes provides insights into strain-specific genes and resolves metagenomics data down to the strain level. Frontiers in Microbiology 9:63. 10.3389/fmicb.2018.00063.

Publications that relied on an early prototype/mentioned the concept

  1. Čuklina J, et al. 2016. Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation. BMC Genomics 17:302. 10.1186/s12864-016-2602-9.
  2. Nesvizhskii AI. 2014. Proteogenomics: concepts, applications and computational strategies. Nature Methods 11:1114-1125. 10.1038/nmeth.3144. Review.
  3. Carlier AL, Omasits U, Ahrens CH, Eberl L. 2013. Proteomics analysis of Psychotria leaf nodule symbiosis: improved genome annotation and metabolic predictions. Molecular Plant-Microbe Interactions 26:1325-1333. 10.1094/MPMI-05-13-0152-R.
  4. Omasits U, et al. 2013. Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome. Genome Research 23:1916-1927. 10.1101/gr.151035.112.