Need help to generate custom MS database using CustomProDB?

Question

[nattzy94]

Hi,

I am having some trouble with generating a custom MS database using the R package CustomProDB. The main function for generating the custom db is 'Outputproseq' which takes the following inputs:

1. rpkm: a numeric vector containing RPKM for each protein.
2. cutoff: User-defined cutoff value for RPKM.
3. proteinseq: a dataframe containing protein ids and protein sequences.
4. ids: a dataframe containing gene/transcript/protein id mapping information

I have items 1, 2 and 4. However, I am having trouble generating item 3, the dataframe of protein ids and protein sequences. Does anyone know how to generate this df? Or can anyone point me to some kind of resource?

The CustomproDB manual does not provide information on how to obtain this df.

[Ram]

Please post this question on bioconductor support. I'd also recommend emailing Bing Zhang.

[nattzy94]

Okay, will do. thanks!