trypsin digestion of 2D-PAGE protein spot - (Oct/18/2014 )

I lyophilized tryptic protein digestion (2D-PAGE spots) and sent them for mass spectrometry (MS) but there is problem to resolve them to continue for MS because  MS result showed a decreased number of picks/fragments for BSA as a control spot as well as other protein spots. Is it possible the peptide fragments bind strongly to vials and do not resolve?  

If I understand that correctly, your problem is that you get a too low number of fragment spectra from a BSA control that you digested alongside your actual sample? If you stored your peptides in re-suspended form in an Eppendorf tube, binding to the tube might be a problem (ask your MS lab for advice on special low-binding glass vials or store without re-suspension after lyophilization). If you had a nice Coomassie visible spot, I however doubt that binding to the tube is sufficient to explain a failed MS analysis.

Was this silver stained gel or coomassiae stained? Peptides binding to the tube is very unlikely. Anyways before mass spec, they will resuspend it in acetone and water, right? It should come, may be in less amount but loss should not be too much, as michael_P also pointed out, this reason is not sufficient to explain a failed MS analysis. Was your trypsin digestion efficient?

Oh I dint see this post is quite old.