Your task can be more easily handled by using a hash rather than an array. When you say that the data is in an tab-separated array, do you mean that you have a file which consists of tab-separated lines containing the data? Since you only want to keep one entry for each ID, then a hash containing a reference to an array holding the organism and number values will be a good way to go. Do you have any code we can help you with? Check out the Tutorials section if you need to read up on the data types.

Update: A skeleton which will read in your data line by line...

#!/usr/bin/perl
use warnings;
use strict;

my %proteins;

while (my $line = <DATA>) {
  chomp $line;
  my ($pro, $org, $value) = split '\s+, $line;  # \s+ : one or more wh
+itespace chars
}

__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
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