I'm not sure I understand the question - why would your attempt be only finding the 5th in the list - if you're attempting to preclude the possibility of a leading '>', then surely both the 4th & 5th elements of the list should be 'found' - unless of course the snippet is a little too small...

Either way, suitable use of \s* would suffice, such that the snippet might become...

while (<DATA>) {
    chomp;
    next if /^>\s*/;
    print "MATCH => $_\n";
}

__DATA__
>Sensor30
>FooSensor30
> Sensor30
Sensor300
Sensor30
>Sensor3
[download]

Note that inverting the sense of the makes the test for whitespace redundant since the next will be executed whenever the line begins with a '>'. To avoid any line whose first non-whitespace char, change /^>\s*/ to /^\s*>/.