Some issues about the example and MzTransform() function

[YonghuiDong]

Hi Zhiwei,

I am amazed by your nice work.

I enjoyed reading your publication. It is so comprehensive and informative. You work and the webserver is of great help to many of us!

When I checked your R package, I found most of the examples within the functions are not executable. Could you please check them?

For instance:

• Installation of the package should be devtools::install_github("ZhuMetLab/AllCCS")
• in MdGet() function, the parameter status_label is not described. id_allccs column does not exist for test data.
• the m/z transform function is named as MzTransform, while in the example, it is called by mz_transform.

In addition, I have some doubts regarding MzTransform() function. It seems that the calculated m/z values are not correct.

For instance:

MzTransform(formula="C100H500OH", adduct = '[M+Na]+', polarity = 'pos')

output:

 M  adduct            mz
 1 1721.91879716 [M+Na]+ 1744.90809716

While the correct monoisotopic mass for this mass formula should be 1743.9044.

When the mass is small, the m/z difference is trivial, but the mass difference becomes obvious for compounds with bigger molecular weight.

Thanks again.

Dong

[JustinZZW]

Hi Dong,
Thanks a lot for your kindness comment and feedback. The repository here is only the example of source code for demenstration purpose. Some related descriptions, manuals and examples were not updated yet, and some internal .rda files were not included. Personally, I'd be willing to share the all codes and internal .rda with you. But, as you may guess, I don't have the full authority.

Could you visit our web server to use prediction functions? We will provide API for convenient use in the future.

For the monoisotope mass calculation, I agree with your comment, and thanks a lot for your correction. In AllCCS, the calculation was performed via Rdisop package. I didn't found obvious differences in our work, because we mainly focus on small molecules (mass <= 1200). I will fix it in the package ASAP.

Finally, I don't recommend to use AllCCS to predict CCS values for polymers (e.g. peptides, polysaccharide etc.). They are not covered in our training set. So, the appliable mass range was limited as 60-1200.

Best,

Zhiwei

[YonghuiDong]

Hi Zhiwei,

Thanks for your explanation.

I have tried with the webserver. It works very well!

Thanks again.

Dong