This very understated paper in JPR may be the biggest advance in phosphoproteomics since the neutral loss scan. This method outlines a new method, dubbed FACE, for Filter Aided Capture and Elution.
1) Digest all of your peptides
2) Incubate your peptides with an anti-phospho- antibody (they used 3G10 anti-phosphotyrosine)
3) Spin your peptides through a size-exclusion column. The unbound peptides flow right through, leaving only the antibody and bound peptides
4) Wash to remove all unbound peptides
5) Elute your phosphotyrosine peptides using acid.
I see almost unlimited promise in this method. I asked around and there are anti-phosphoserine and -threonine antibodies, but they are generally regarded as no good.
I will be trying this method very soon, considering phosphoproteomics is what I was hired for.