use strict;
use warnings;

while (<DATA>) {
    if (/^(\d+\D\d)_(LacZ|pgK|SD|SU)(.*)$/) {
        print "match: $_";
        print '    $1', " is $1\n";
        print '    $2', " is $2\n";
        print '    $3', " is $3\n";        
    }
    else {
        print "no match: $_";
    }
}

__DATA__
12774L1_LacZ.SEE.rc_C06_2008-12-01.ab1
12774L1_pgK.Neo.2fw_D06_2008-12-01.ab1
12774L1_SD_B06_2008-12-01.ab1
12774L1_SU_A06_2008-12-01.ab1
foo.bar
[download]

prints:

match: 12774L1_LacZ.SEE.rc_C06_2008-12-01.ab1
    $1 is 12774L1
    $2 is LacZ
    $3 is .SEE.rc_C06_2008-12-01.ab1
match: 12774L1_pgK.Neo.2fw_D06_2008-12-01.ab1
    $1 is 12774L1
    $2 is pgK
    $3 is .Neo.2fw_D06_2008-12-01.ab1
match: 12774L1_SD_B06_2008-12-01.ab1
    $1 is 12774L1
    $2 is SD
    $3 is _B06_2008-12-01.ab1
match: 12774L1_SU_A06_2008-12-01.ab1
    $1 is 12774L1
    $2 is SU
    $3 is _A06_2008-12-01.ab1
no match: foo.bar
[download]

Update: Furthermore, grep properly filters out the "foo.bar" file I injected:

use strict;
use warnings;
use Data::Dumper;

my @files = qw(
    12774L1_LacZ.SEE.rc_C06_2008-12-01.ab1
    12774L1_pgK.Neo.2fw_D06_2008-12-01.ab1
    12774L1_SD_B06_2008-12-01.ab1
    12774L1_SU_A06_2008-12-01.ab1
    foo.bar
);
print Dumper(\@files);
@files = grep /^(\d+\D\d)_(LacZ|pgK|SD|SU)(.*)$/,@files;
print Dumper(\@files);

__END__
$VAR1 = [
          '12774L1_LacZ.SEE.rc_C06_2008-12-01.ab1',
          '12774L1_pgK.Neo.2fw_D06_2008-12-01.ab1',
          '12774L1_SD_B06_2008-12-01.ab1',
          '12774L1_SU_A06_2008-12-01.ab1',
          'foo.bar'
        ];
$VAR1 = [
          '12774L1_LacZ.SEE.rc_C06_2008-12-01.ab1',
          '12774L1_pgK.Neo.2fw_D06_2008-12-01.ab1',
          '12774L1_SD_B06_2008-12-01.ab1',
          '12774L1_SU_A06_2008-12-01.ab1'
        ];
[download]