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A free online tool for protein cleavage sites prediction with a chosen enzyme.
Calculate monoisotopic and average mass of a custom peptide or peptides predicted from a protein.
The cleavage specificities of selected enzymes.
A comprehensive and freely accessible resource of protein sequence and functional information.
Mass spectrum simulation tool for peptide/protein sequences. The number of charge can be custom defined.
An online tool predicts m/z values for SMS ions generated from selected fragmentation methods such as CID, ECD, or ETD. The ion type and maximum number of charge can be pre-defined.
PDB provides the most complete collection of information about the 3D structures of proteins, protein complexes and other biomolecules.
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SEED Technology
SEED (Scrambling-free Electron-based Examination of Deuterons) is the first commercially available platform for determining exchanged deuterons in HDX-MS with single residue resolution using tandem mass spectrometry. The traditional bottom-up HDX-MS workflow can only obtain intermediate resolution by analyzing overlapping peptides because: 1) the digestion enzyme (normally pepsin) does not cut at every amino acid; 2) the number of peptides identifiable by LC-MS is limited due to the relatively short elution gradient used; 3) the back exchange level of the peptides are different from each other. To further increase the resolution, an interesting option is to apply a gas-phase fragmentation method inside the mass spectrometer (MSMS) so that residue-specific information can be possibly achieved. However, the occurrence of hydrogen scrambling resulting from an interchange of protons and deuterons among all exchangeable sites within the peptide/protein precludes the use of collision-based dissociation such as CID, the most widely used gas-phase fragmentation technique, as a general MS method to obtain information about protein solution deuteration patterns [1,2]. The H/D scrambling mechanism is summarized in Figure 1.
Electron based fragmentation showed great potential in obtaining residue-level HDX information, however, many experimental and instrumental factors can still cause excessive vibrational excitation of the protonated peptides during peptide ion transfer and the fragmentation process and lead to H/D scrambling [3,4], thus special caution needs to be taken when performing this kind of experiments and analyzing the data. NovoAb scientists have pioneered the research in this field and are highly experienced in analyzing the HDX-MSMS data from all kinds of proteins including antibodies. Along with the use of the newest generation fourier-transform mass spectrometric instruments, our proprietary SEED technology platform allows for unambiguous determination of the correct deuteration pattern with amino acid-level resolution (Figure 2).
References
1. Harrison, A. G.; Yalcin, T. Int. J. Mass Spectrom. 1997, 165, 339–347.
2. McLafferty, F. W. et al. J. Am. Chem. Soc. 1998, 120, 4732–4740.
3. Rand, K. D. et al. J. Am. Chem. Soc. 2008, 130, 1341–1349.
4. Pan, J. et al. J. Am. Chem. Soc. 2008, 130, 11574–11575.
