I am new to R and MSnbase. I am trying to generate the impurities matrix for correction for a TMT 10-plex experiment.

The correction from Thermo are as follows in a csv file (lot: WI319139).

.,-2,-1,1,2
126,0,0,7.4 (127C),0 (128C)
127N,0,0,7.2 (128N),0 (129N)
127C,0,0.8 (126),6.9 (128C),0.1 (129C)
128N,0,1.2 (127N),6.3 (129N),0 (130N)
128C,0 (126),1.3 (127C),5.7 (129C),0.1 (130C)
129N,0 (127N),1.5 (128N),5.7 (130N),0.1 (131)
129C,0.3 (127C),2.7 (128C),4.8 (130C),0
130N,0 (128N),2.2 (129N),4.6 (131),0
130C,0 (128C),3.1 (129C),3.6,0
131,0 (129N),8.7 (120N),3.4,0

This matches to what is mentioned in the documentation

I try to makeImpuritiesMatrix using the following:

impurities <- makeImpuritiesMatrix(filename = "./TMT_impurity_matrix.csv")

But I get the error: Problem reading impurity matrix. Not square.

I read somewhere we can add more columns to the left and right (i.e. -3,-4,-5, .. , 3, 4, 5) but then it does not transform the corrections to the correct isotopes.

I also could not find any example csv file for the TMT 10-plex in the extdata folder (https://github.com/lgatto/MSnbase/tree/master/inst/extdata)

Can someone please help with how to generate the impurity matrix for such a file?

As the message says, the matrix must be square - yours has dimensions 10 by 4 (after removing the row names). There is no TMT10-plex example, but the TMT6-plex example should help you to get there, filling in the 0 to get your 10 by 10 matrix. You can also simply run impm <- makeImpuritiesMatrix(10) and then fill in your own values.