My expressed proteins are frequently truncated and I'm trying to figure out which bands are which. The first thing to come to mind is using PeptideCutter from ExPASy but there is just a data deluge of potential sites. I was curious what other strategies exists for determining the potential breaks asides using LC-MS.
LC-MS is certainly quantitative and will give you a definitive answer, but it is costly and requires access to such a machine.
I presume you're analyzing your protein based on western blotting.
The first thing you should always do is verify your DNA sequence is coding for the protein product you want. Once you're sure of this, the western blot will give you an indication as to where your protein is (approximately) being cleaved. Say you protein has a predicted size of 40 kDa and you see a band at 20 kDa, then your cleavage is somewhere in the middle of your sequence. There are a TON of proteases that could be potentially cleaving your peptide and you need to have a hypothesis as to what that could be. Your peptide could be cleaved by an endopeptidase (cutting within), or a carboxypeptidase (C-terminal cleavage) or an aminopeptidase (N-termainal cleavage). To go back to the 20/40 kDa example, it could be your peptide was cleaved N-terminally o C-terminally down to a size of 20 kDa, or that it was literally cleaved in the middle by an endopeptidase.
Something you may consider is the use of a general protease inhibitor cocktail (Roche makes a really good tablet product called Complete and Complete mini tab). These mixes have a bunch of general protease inhibitors which will stop most cleavage events. If you still see cleavage after using an inhibitor cocktail, you can reasonably expect that you are not inhibiting the protease with the tablet (thus narrowing down your search) and then you can better comb through Expasy's PepCutter data. You should also do a literature search to see what has been reported about your peptide or motif.
You could also try induction at lower temperatures to minimize chances of protein degradation. Cells such as Arctic cells (http://tinyurl.com/arcticecoli) are optimized for low temperature expression although BL21 works just as good for the proteins we express (upto 140kDa in size)
One way to learn more about how your protein is being processed/degraded is to add two different tags on either end of your protein. Express your protein, then blot with the two antibodies for your tags. The most likely scenario here is that one end or another is being cleaved and then degraded - you'll be able to tell which end by what tag epitope remains. And since you'll know the approximate size, you can narrow down the region where the processing occurs.
Small tags such as HA, cMyc, Flag or 6xHis work well because they are less likely to be cleaved off themselves.
The only way to know for certain how and where your protein is being truncated is empirically: either by N-terminal sequencing of the fragment(s) by mass spec or by mutating the putative processing sites and testing the expression again.