Your limitations will not be those of instrument sensitivity. A MALDI-TOF instrument of recent vintage has fmol sensitivity. You do need to be clear - you say 'peptide samples' I'm presuming you mean 'protein samples'? I also presume you want to know the identity of the protein band?

As a rule of thumb, a band that is visible with Coomassie Blue staining should be fine for MALDI-TOF after in-gel digestion. The protocols for in-gel are well worked out, but I would have a little caution about leaving the gel pieces in water. Use destain solution perhaps?

if the band is only detectable by silver stain, then expect problems. Keratins will dominate the spectra! Also, some silver protocols actually fix the protein and make it harder to analyse.

The lab to which you are sending your samples should have given you very detailed instruction on gels,protocols etc. You would be well advised to seek out these instructions.

Otherwise, they may charge you and you'll get no data, or you will find that the analytical lab is less likely to work on your samples, if they are consistently seeing keratin as the main protein! For example, home-made gels are MUCH worse for keratin contamination than home made gels. Gloves at ALL times. Don't leave gels on open benches. All obvious, but not if you're just running gels to visualise proteins.

One last point. If you are working with a n organisms for which an annotated proteome does not exist, expect to work harder, possible needing MALDI-TOF/TOF, for partial sequence tags as well.

Generally MALDI-TOF requires very little protein, in the range of hundreds of pmoles. I suppose the required amount varies between instruments and used matrices but if you can see a band with coomassie staining it should be enough. Keep the gel piece in water so that it stays hydrated - the protein should not get extracted, although very small proteins (less than 10k) might actually elute away from the piece.

Distilled water is fine. Generally, 1-100 pmol is required. As a good rule of thumb it should be detectable as a stained band with appropriate staining.

If you are running SDS-PAGE analysis you will likely be performing in-gel trypsin digestion. It is very difficult to extract intact proteins from gela for intact protein analysis. If you are wanting MS-MALDI analysis on your intact protein you are best off with the protein in low salt conditions and free of detergents.

-please excuse typos a ind brief answers as this was sent from a smart phone.

It is possible to elute larger proteins by electroelution but MALDI-ToF has limitations for large proteins. 1ul sample+1ul matrix is fine for most MALDI-ToFs..!!