if $a[0] has rowspan=2 then we have to place one empty <th></th> in the corresponding place of $a[1]
if rowspan=3 the we have to place empty <th></th> in $a[1] and $a[2] in corresponding place.

##</code><code>##

#!perl ;
use strict ;
use warnings ;

my @a ;
my @b ;
my @c ; 
my @splitted ;
my $i ;
my $j ; 
my $aref ;

$a[0] = "<th><rowspan=2>Target protein</th><th><colspan=2>Purified protein concentration</th><th><rowspan=3>Activity</th>" ;
$a[1] = "<th>Mg/liter culture</th><th>Mg/g dry cell weight</th>" ;
$a[2] = "<th>Mg/liter culture</th><th>Mg/g dry cell weight</th>" ;

# First build an array of array

foreach $i (0..$#a) {

	@splitted  =  $a[$i] =~ m#(<th>.*?</th>)#g   ; 
	$b[$i][$_] = shift @splitted  for  (0..$#splitted )  
	
}

# Apply rules

$aref = $b[0];

for $j ( 0 .. $#{$aref}  ) {

	if  ( $b[0][$j] =~ m/rowspan=(\d)/  &&  $1 == 2 ) { 	
	
		$b[1][$j] = "<th></th>" . $b[1][$j]  ;
	
	}
	
	elsif ( $b[0][$j] =~ m/rowspan=(\d)/  &&  $1 == 3 ) { 	
	
		$b[1][$j] = "<th></th>" . $b[1][$j] ;	
		$b[2][$j] = "<th></th>" . $b[2][$j]  ;	
	}
	
}

# Merge into a simple array

for $i ( 0 .. $#b) {
      
	$aref = $b[$i];
        
	$c[$i] = join "", @$aref ;
	
}
	
# Format and print result 

 foreach (@c) {$_ =~ s#</th>#</th>\n#g;   print $_, "\n\n" ;  }
	
##</code><code>##

<th><rowspan=2>Target protein</th>
<th><colspan=2>Purified protein concentration</th>
<th><rowspan=3>Activity</th>

<th></th>
<th>Mg/liter culture</th>
<th>Mg/g dry cell weight</th>
<th></th>

<th>Mg/liter culture</th>
<th>Mg/g dry cell weight</th>
<th></th>