Like CountZero already pointed out:

chomp(); # remove the newline from $_;
$peptide = $_; # Current peptide (line) being checked
push(@peptides, $peptide); # Adds each peptide to an array (note the s
+ingular/plural)
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The thing is, if you want the last element of an array, you need to do: $peptide = $peptides[$#peptides]

Alternatively, you can write both assignments in a single line:

push(@peptides, $peptide = $_);