I tried this:

my $str="Study Protocol Number NBXF317N2201"; 
my ($term) = $str =~ /Protocol (?:(?:No\.|Number)? )?([A-Z0-9]{12})/; 
print $term;
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Another question: do you mean the . after No to be optional? Then it has to be

my $str="Study Protocol Number NBXF317N2201"; 
my ($term) = $str =~ /Protocol (?:(?:No\.?|Number) )?([A-Z0-9]{12})/; 
print $term;
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UPDATE: Having thought about it, I would do the following which IMHO is simpler to read:

use strict;
use warnings;
for my $str ( "Study Protocol Number NBXF317N2201", 
        "Study Protocol No. NBXF317N2201",
        "Study Protocol NBXF317N2201",
        "Study Protocol No NBXF317N2201" ) { 
        my ($term) = $str =~ /Protocol (?:No\. |No |Number |)([A-Z0-9]
+{12})/; 
        print "$term\n";
}
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