Support normalization using multiple reference proteins

[OlgaTSchubert]

Hi David,

It would be great if we could use multiple reference genes at once (I think MSstats does accept a vector of genes for this, see "nameStandards" in MSstats manual).

When I tried to give a vector in the config file for artMS I got the following error:

Error in dataProcess(raw = dmss, normalization = config$msstats$normalization_method, : global standard peptides or proteins, c("YFL039C" , is not in dataset. Please check whether 'nameStandards' input is correct or not

Thank you! Olga

[biodavidjm]

Hi Olga,

it turns out that artMS supports that feature as well. You just need to provide the list of protein ids comma separated. For example, if you want to use these two proteins Q86U42, O75822 as reference for normalization, in the yaml file, msstats section, you would write:

  normalization_method: globalStandards
  normalization_reference: Q86U42, O75822

Please, give it a try and let us know if there is any problem.

And thanks for the feedback. We will update the artMS documentation in the next release to make it more clear.

[OlgaTSchubert]

Hi David,

Thanks for looking into this. Great to hear that it actually works already!

Many thanks and best wishes, Olga

[OlgaTSchubert]

Hi David,

I just wanted to report that I tried this with multiple genes and it worked well.

Thanks, Olga

[biodavidjm]

Thanks!