use strict;
use warnings;
use Data::Dump::Streamer;

my @array = <DATA>;

chomp @array;

my %uniq;

for (@array) {
     my @parts = split "\t";
     
     next if @parts < 3;
     next if exists $uniq{$parts[0]} and $uniq{$parts[0]}{val} < $parts[2];
     $uniq{$parts[0]} = {val => $parts[2], data => $_};
}

Dump (\%uniq);

__DATA__
protein1	organism1	0.843534
protein2	organism2	2.45
protein3	organism3	9.5322
protein4	organism4	0.3475474
protein1	organism6	9.4534
protein2	organism7	0.43534
protein2	organism8	1.2434
protein3	organism9	0.000003
protein3	orgnanism10	1.23325