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30th Nov 2006
Manuscript Number:MSB-06-261R
Title:Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe
Author:Dieter Wolf
Michael Schmidt
Andres Houseman
Alexander Ivanov
Dear Prof. Wolf,
Thank you for sending us a revised version of your manuscript. I am pleased to inform you that the initial impression of your manuscript is favourable and it may be acceptable for publication pending the following minor modifications:
1. We are still not convinced that the comparison between your study and the ORFeome study by Matsuyama et al (see Suppl Fig 3) is highly relevant. As you mention, Matsuyama et al (Nat Biotechnol. 2006 Jul;24(7):841-7) cloned all ORFs (ATG to penultimate codon) under the control of the same nmt1 promoter. Presenting the ORFeome (a "localisome" study) as a protein quantitation experiment is in fact rather misleading and the absence of correlation with your datasets seems absolutely logical since the mere principle of the ORFeome experiment (that is the use of a standardized expression cassette) precludes *by design* any correlation with endogenous expression levels. Under these conditions, we have difficulties seeing what insight can be gained from the direct comparison pombe-mRNA vs. pombe-ORFeome and even pombe-ORFeome vs. pombe-ASC. Could we suggest to remove this part of the analysis?
2. Referee #1 suggests to add a few lines of justification on your microarray strategy (see referee #1 comment below)
3. The URL link to GeneDB should be removed from the reference list and provided directly in the text.
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Reviewer #1 (Remarks to the Author):
The authors present a detailed response to all issues raised by the referees. Some of this is a bit of a smokescreen, masking how few substantial changes have actually been made in the manuscript itself. In general, however, I am satisfied with the changes made or the justifications provided for not making changes. The manuscript should be suitable for publication, subject to a minor addition described below.
1) Issue 4, referee 1: Some of this rebuttal is factually wrong. A search on the Affymetrix website will show that there are both ORF and tiling chips for S. pombe, and the use of genomic DNA as a reference is widely accepted (see for example papers of Pat Brown's lab). It would have been interesting to see whether the correlation between mRNA and protein levels increases when using DNA as a reference, given that the authors went through all the troubles to recalculate the data (without adding any of this into the manuscript). Anyway, I do not request that the estimation of mRNA levels has to be done in a different way, but at least the authors should briefly justify their approach in the manuscript (using a shortened version of explanations and references provided in their rebuttal, point 4b).
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