Depends on what you are looking for. These two techniques are basically complentary. 2DE offers the separation on protein level, enabling analysis on protein isoforms, when multiple protein spots were identified as the same proteins, while quantification done using LC-MS/MS somehow is more reproducible since less laborious processes are involved.

They are both good methods but will give different results. Have a look at this example from one of my colleagues.

http://blog.nonlinear.com/2012/05/09/label-free-lc-ms-and-2d-gel-electrophoresis-complementary-approaches-to-increase-proteome-coverage/

I agree with Siyan and Andrew. Both techniques are interesting and complementary for global proteomics approaches. We have successfully used a combination of these techniques and obtained a reference proteome ( http://www.ncbi.nlm.nih.gov/pubmed/21078152 ) and also carried out a differential label free nanoLC-MS/MS study ( http://www.ncbi.nlm.nih.gov/pubmed/23119012 )

There is also an intermediate that provides an extremely robust platform for proteomics, GeLC/MS/MS, i.e. separation of proteins by SDS-PAGE or non-denaturing PAGE, followed by LC/MS/MS analysis of gel slices. Provided you have access to a reasonably powerful nanoLC/MS/MS instrument for analysis, It is easily compatible with traditional protein analysis techniques such as Western Blotting, IP or others.

It should be mentioned that the resulting gel slices should be in-gel digested and the resulting peptides extracted prior to nanoLC/MS/MS