Editor Yang's Offer to correct and discussion

Editors offer to correct and discussion

On Tue, Jan 31, 2023 at 9:32 PM Mr. Zack Yang / MDPI wrote:

Dear Chris and Felice,

Thank you for your email. Your description of the two protocols "IROA Workflow" vs "IROA TruQuant Workflow" explains the fundamental misunderstanding and miscommunication that has occurred. It further explains why the authors' rebuttal has been focused on relative quantification, while your criticism has been focused on absolute quantification.

We believe the best course of action is for the authors to publish a correction that includes changing the term "IROA TruQuant Workflow" to "IROA Workflow" and explaining the differences between the two protocols and their purposes. The authors should also include the raw data.

We also invite and strongly recommend that you publish a Comment to their article and we will invite the authors to reply. This will afford you the opportunity to highlight what the newer "IROA TruQuant Workflow" can do.

A healthy open scientific discussion has the best chance to illuminate better or even best practices on these types of samples. But patience is needed to work through miscommunication.

Looking forward to your reply.

Best regards, Zack Yang Managing Editor, MDPI 

Reply to Offer to correct

On 2023/2/2 6:23, Felice de Jong wrote:

Dear Editors Zack and Moseley,

We thank you for your most recent letter and recommendations but insist that three conditions should be met before we can agree:

1) The paper on the web has been viewed from over 700 different web addresses and your statistics show it is getting approximately 3 views per day.  We cannot have this manuscript continue to be publicly available during the time period that all of these changes are being organized and prepared.  If this article is not to be retracted, then it needs to be withdrawn from public viewing from now until such time as the revised article and the attachments are finalized. Another option is to leave the title only together with a subtitle that states: “This article has been temporarily removed while revisions are being made”.

2) In order to expedite this process, we will commit to submitting our comments within four weeks of receiving the full dataset, and within two weeks after receiving the author’s revision.  If the author sends us the data immediately and can complete their revisions quickly the article could be live again by early March.

3) The authors must make it very clear that they did not follow the IROA TruQuant workflow, and that they made no attempt to balance the Internal Standard concentration to their samples.

We still have reservations concerning 1) the author’s method of calculating ratios and their use in the statistical analysis, and 2) the diluted nature of the samples. We are willing to address these concerns in our comments provided we gain access to the data which was promised by the authors.

Sincerely,

 *Felice A. de Jong, PhD, CEO*

Editor Zack's reply to request for period of suspension

 On 2023/2/2 6:23, Zack Yang wrote:

 Dear Felice,

Thank you for your prompt reply.

As for the first point you mentioned, I am sorry that we cannot hide the original article. The paper's issue has been released, the version available is taken to be definitive, called the ‘version-of-record’. This version is taken by indexing databases and any changes must be formally and publicly announced.  I fully understand about your concerns, thus, we agreed with your proposal to publish a Comment and Reply which will be linked with the original paper so that readers will know the whole picture.

As for second point and third point, we can discuss them with the author immediately and ask them to provide the original data for you. You can quickly assess and publish a formal Comment. We will contact the author to revise their paper according to your comments and then provide a Reply. Comments and Reply will link to the original article page. (e.g. https://www.mdpi.com/2218-1989/11/9/596) Please check the details enclosed. In this way, readers can learn more about IROA TruQuant workflow based on the content in the Comment and Reply. What do you think?

Looking forward to hearing from you.

Best regards,

Zack Yang

Managing Editor, MDPI Wuhan