Issues with your program:

• Your data is tab-separated, but you split on blanks.
• The newline is included in your array

After solving these, the question remains what you want to achieve with $sum. You try to add the string contents of your array resulting in the warnings you see.

Without knowing what kind of sum you want, I cannot help at this point. As far as you described the task, this would do:

#!/usr/bin/perl

use strict;
use warnings;

my @content = (<DATA>); 
my @myArray;

for my $row (@content) {
    chomp $row;
    my @columns = split "\t", $row;
    push @myArray, \@columns;
}

my $title_row = shift @myArray;

for my $row (@myArray) {
    print join('; ', @$row), "\n";
} 

__DATA__
ProteinName    MF1    MF2    MF3
GH1    Growth factor activity    Growth hormone receptor binding    Ho
+rmone activity
POMC    G protein-coupled receptor binding    Hormone activity    Sign
+aling receptor binding
THRAP3    ATP binding Source    Nuclear receptor transcription coactiv
+ator activity    Phosphoprotein binding
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