Tissue samples in biobanks are typically formalin-fixed and paraffin-embedded 
(FFPE), in which form they are preserved for decades. It has only recently been 
shown that proteins in FFPE tissues can be identified by mass spectrometry-based 
proteomics but analysis of post-translational modifications is thought to be 
difficult or impossible. The filter aided sample preparation (FASP) method can 
analyze proteomic samples solubilized in high concentrations of SDS and we use 
this feature to develop a simple protocol for FFPE analysis. Combination with 
simple pipet-tip based peptide fractionation identified about 5000 mouse liver 
proteins in 24 h measurement time-the same as in fresh tissue. Results from the 
FFPE-FASP procedure do not indicate any discernible changes due to storage time, 
hematoxylin staining or laser capture microdissection. We compared fresh against 
FFPE tissue using the SILAC mouse and found no significant qualitative or 
quantitative differences between these samples either at the protein or the 
peptide level. Application of our FFPE-FASP protocol to phosphorylation and 
N-glycosylation pinpointed nearly 5000 phosphosites and 1500 N-glycosylation 
sites. Analysis of FFPE tissue of the SILAC mouse revealed that these 
post-translational modifications were quantitatively preserved. Thus, FFPE 
biobank material can be analyzed by quantitative proteomics at the level of 
proteins and post-translational modifications.