Response to Comment on "Deep Proteogenomics of a Photosynthetic Cyanobacterium"

This letter responds to the manuscript by Liu et al., in which the authors comment on our work previously published in JPR (Deep Proteogenomics of a Photosynthetic Cyanobacterium. J. Proteome Res. 2023, 22, 1969. DOI: 10.1021/acs.jproteome.3c00065). After carefully reading their manuscript, we identified several problems with its content. The authors have overlooked or misunderstood several procedures in our proteogenomics workflow, misinterpreted several findings, and, consequently, drew partially wrong conclusions. A direct comparison of their analysis with our published data shows that their results largely confirm our conclusions. For five of the six ORFs they discuss, most notably for sll1911, their findings are fully consistent with our peptide evidence and with updated UniProt or NCBI annotations. In the remaining case, our results agree with established reference annotations and previously published MS studies. In our opinion, the criteria for "deep proteogenomic annotation" proposed by Liu et al. largely reiterate existing standards. To conclude, their letter does not contradict our findings, but instead reflects misunderstandings of our data presentation and methodology.