"unique == hash". Consider:

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} < $part
+s[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
[download]

Prints:

$HASH1 = {
           protein1 => {
                         data => "protein1\torganism1\t0.843534",
                         val  => 0.843534
                       },
           protein2 => {
                         data => "protein2\torganism7\t0.43534",
                         val  => 0.43534
                       },
           protein3 => {
                         data => "protein3\torganism9\t0.000003",
                         val  => 0.000003
                       },
           protein4 => {
                         data => "protein4\torganism4\t0.3475474",
                         val  => 0.3475474
                       }
         };
[download]