Enhancing Metabolite Coverage in MALDI-MSI using Laser Post-Ionisation (MALDI-2).

Minor 1. Italicize all of the m/z labels. 2. Including more data availablily sources such as information on the statistical analysis code used, would be helpful to the readers. 3. Additional details in the abstract to better guide the problem and how the application of MALDI-2 addresses this issue would better define the purpose of the paper. 4. Justification of the use of only negative mode MALDI-2 in the experiments aside from reference 23 and the same for the choice of matrices used as opposed to the others listed as “commonly used.” 5. In the introduction, reference 30 was used as an example of increased annotations in MALDI-2 over MALDI, but this example was done in the positive mode so if the negative mode is claimed to be the more commonly used, then a negative mode example would be a better fit to this section. 6. The inclusion of fold change data in the main figures could be useful. Note though, that in Table S1, the fold change seen in the smaller m/z (<500) was smaller than those in the higher m/z (>500) which doesn’t entirely support the claim that MALDI-2 collects more annotations at greater intensity than MALDI. 7. Figures S4, S5, and Table S2 would be beneficial as main text figures if it was decided to go the biologically relevant annotations route over MALDI vs. MALDI-2. 3/3

Major 1. Regarding Figure 2, more clarity is needed on the database datasets and their experimental conditions/significance, but more importantly, it may be an unfair comparison to compare annotations from different tissue types, instruments, and different species. When comparing the experimental MALDI-2 mouse kidney annotations to the Human kidney dataset, the experiment appears to fall short in the number of annotations detected, but arguably these datasets should not be compared. When the experimental MALDI-2 mouse kidney annotations are compared to the other Mouse dataset, it better supports the claim that MALDI-2 results in a greater number of annotations in similar experimental conditions than MALDI. As is, Figure 2 is confusing to interpret. 2. In Figure 1a, some points on the chromatogram appear to show MALDI intensity to be higher than in MALDI-2 or places where there is a MALDI peak, but it is absent in MALDI-2. Some explanation to address why this occurred would be beneficial. 3. If the overall aim of the paper is to compare MALDI to MALDI-2, it would be better to compare the number of annotations between the two in both negative and positive mode. If the goal is better identification of small molecular weight metabolites in tissue samples in negative mode then it would be better to focus on relevant annotations as opposed to all. 2/3

In this preprint by Mckinnon et al, the authors introduce a new application for MALDI-2 for the purpose of identifying biologically relevant small molecules in tissue samples. They propose that by using this technique one can identify a broader scope of metabolites in order to compare healthy tissues to their disease-state counterparts. Figures 1 and 3 were very informative and helpful in supporting the hypothesis, but the addition of some extra information, as listed in the SMART guidelines 10.1002/jms.4904 would increase transparency for readers. A major critique was, given the broad title of the paper, that there was some misalignment in the scope of the experiment conducted. This could be resolved by altering the title and abstract to better reflect the selective use of negative mode IMS on tissue samples or an expansion of the experimental scope. It may also be beneficial to focus on the potential biological significance of the annotations or to list all annotations from the experiments to compare the number of annotations. Overall this was a well-written manuscript, but the alignment with the purpose and data could be better aligned so that the conclusion is fully supported by the data. Below please find the following critiques for the authors' consideration. 1/3