Hello,

I am very new to proteomics data analysis. I have a proteomics data set which looks like the below example:

Proteins a b c d Protein 1 57038.57 75498.98 223940.89 47389.90 Protein 2 92730.64 NA 83930.36 434893.34 Protein 3 NA 84930.45 783.37 8903.23 Protein 4 83929.36 NA NA 74830.03

I am not sure how to proceed with the normalization process because of the "NA" values. I tried to get some information regarding this and in some cites it is mentioned to change NA to "0" or to assign values like 0.0001 to NA. Could someone please guide me which is best method to do the normalization and which R package would you prefer for the same?

Many thanks in advance

• First, you need to assess how many missing values you have.
• I would recommend not to impute your data by 0 (or any arbitrary small value) and use it as it is. You should be able to do everything you need.
• This (and references therein) might be useful to get you started: https://rformassspectrometry.github.io/docs/sec-quant.html