Mass-spectrometry based Protein Identification methods available from DC Biosciences.
Because individual proteins are large molecules, they generate complex isotopic envelopes in MS analysis. Thus, it is better to digest complex protein mixtures into smaller peptides, which can then be fragmented to generate MS2 spectra. This strategy is called “bottom-up” proteomics.
Since MS2 spectra can rarely be fully sequenced into parent peptides, database searching is then used to convert them into expected peptide sequences. De novo sequencing is still required in the rare event that expected protein sequences are unknown.
To enhance the fidelity of peptide-spectrum-matching it is considered good practice to observe at least 2 different peptides for a protein to be identified with confidence.
For low-complexity samples – such as when checking the purity of an isolated protein – it is possible to work with intact proteins.