about the mass spectometry - protein vs peptide (Jan/17/2007 )

I would like to knoe what is the difference between the usage of protein or peptide that good for mass spectrometer analysys?

Could anyone tell me that what is the pro and cons between the protein and peptide mass analysis?

Thanks!

Mass Spec is just like a huge and very sensitive balance. Fragmentation patterns compared to libraries enable you to compare and identify your unknown mass. Methods are available for both proteins and peptides. One thing to consider is whether or not your analyte needs pre-anlaytical extraction or protection of vulnerable groups. (which probably ocurs more with lipids/ steriods etc than with protein/peptide). So it may not be the analysis itself so much as the pre-analytical steps that are important. If your analyte is a protein, analyse a protein. If it is a peptide, analyse the peptide. As far as possible. The less you have to do to your analyte the better.