#!/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 whitespace 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