Review of Comparison of urine proteomes from tumor-bearing mice with those from tumor-resected mice

This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/6781847 . Heng Ziqi et al have asked a basic question about differentiating between the individuals with completely resected tumors and ones without complete tumor resection by comparing their urine proteomes at two different time points. The experiments were conducted on fifteen rats, which were divided into three groups of five rats each. The authors carried out a reasonable scramble analysis to show the significance of their findings. However, I have several major concerns with their work, which I have described below: Major Comments While the authors satisfactorily show that upon complete resection, the urine proteome of the tumor-bearing rats reverts to a state similar to that of the healthy rats, the reverse causality relation is not sufficiently convincing. The authors have not compared their results to a case where the tumor is partially resected. For the completeness of the study, I would suggest the authors to include tumor-bearing rats from a "partial tumor resection" category with partially resected tumor and check if their proteomes show any differences. Also, I would suggest the authors to discuss the assumptions of the study explicitly while describing their conclusions towards the end of results section or in Discussions section. The authors have cited a few studies which indicate that the position of tumor implantation dictates changes in urine proteome. In addition, several other factors also lead to changes in urine proteome. Also, the effect of using another cancer cell line on urine proteome is currently not discussed. I would suggest the authors to check if their results hold when they conduct this study using another cell line. Minor Comments In the second paragraph of Introduction section, the authors have included phrases like "stable and balanced" and disturbing factors, which lack specifics. I would suggest avoid these. In the third paragraph, the ...