Needs more information to work this out-

With regards to the first IP-

Are you using a labelled primary antibody, or a labelled secondary antibody?

Are you using a secondary antibody that only detects native form of the primary antibody, i.e it will only detect the primary antibody used in the western and not the denatured form that has been run in the SDS-PAGE?

With regards to the second IP-

Is this the same IP as before but reprobed on the same membrane?

Or did you repeat the IP with a different antibody, or same IP antibody as before but probed on western with different primary?

Did you use a different secondary antibody this time? 

I would be very happy not to have antibody chains on my IP-western! I am curious, however, as to why you don't have them.

I agree with Amanda: it's a dream not to have any heavy and light chain on the Western! But why? :-)

My guess would be: it's possible that the primary antibody in your first IP is very strong in binding with the beads, staying there and not dissocating when you elute; while the primary antibody in your second IP comes off when you elute/extract your protein.

Can you tell us more about your antibodies ? 

hi,

in terms of heavy and light chain on your blot this can be "removed" by using the TrueBlot secondary Ab (HRP) instead of regular secondary Abs. these will not recognize heavy or light chain on the membrane while labeling. we have used it for a long time and they work very well.

If the primary Ab is covalently coupled to beads such as Dynabeads less will be eluted off if mild elution is used (e.g. low pH). This in combination with TrueBlot have worked very well in our hands as we are working with targets at similar size as heavy or light chain.