Integrated proteogenomics database

When using the iPtgxDB web service, please cite

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

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

Genome Research, 27 , 2083-2095, 2017

Selected publications that used/referenced the iPtgxDB solution

16. Varadarajan AR, et al. 2020. A Proteogenomic Resource Enabling Integrated Analysis of Listeria Genotype-Proteotype-Phenotype Relationships. J Proteome Res. 2020. 10.1021/acs.jproteome.9b00842.
15. Varadarajan AR, et al. 2020. An integrated model system to gain mechanistic insights into biofilm formation and antimicrobial resistance development in Pseudomonas aeruginosa MPAO1. Preprint at bioRxiv.
14. 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
13. Agrawal A, et al. 2019. Global proteome profiling reveals drug-resistant traits in Elizabethkingia meningoseptica: An opportunistic nosocomial pathogen. OMICS 23:318-326. 10.1089/omi.2019.0039.
12. Low TY, Mohtar MA, Ang MY, Jamal R. 2019. Connecting proteomics to next-generation sequencing: Proteogenomics and its current applications in biology. Proteomics 19: e1800235. 10.1002/pmic.201800235. Review.
11. 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.
10. 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.
9. Tong X & Liu S. 2018. CPPred: coding potential prediction based on the global description of RNA sequence. Nucleic Acids Research 47:e43. 10.1093/nar/gkz087.
8. 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. Review.
7. 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.
6. Nanes 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. Review.
5. 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

4. ÄŒuklina 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.
3. Nesvizhskii AI. 2014. Proteogenomics: concepts, applications and computational strategies. Nature Methods 11:1114-1125. 10.1038/nmeth.3144. Review.
2. 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.
1. 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.