The Chemical Modifications view is an advanced feature of the Proteome Discoverer application. You use it to build and maintain the static and dynamic modifications data that is available when you define your search settings.
In the Chemical Modifications view, you can explore the default types of modifications and their corresponding amino acids. This view contains the modification’s delta mass, amino acids, substitutions, neutral losses, diagnostic ions, and, when applicable, cross-linking information. By using the Chemical Modifications view, you can modify existing modifications and create new modifications.
Procedure
- Do one of the following:
- Select Administration > Maintain Chemical Modifications.
- Select Maintain Chemical Modifications
. - The Chemical Modifications view opens on the Administration page. The target amino acids listed are those that can be modified for the specific modification.
- (Optional) To see more detail, select the row with the modification of interest, and select Edit.
- As an example, the following image shows information for the acetyl modification. The following table lists the available modification categories.
Classification | Description |
|---|---|
Post-translational | Protein modification after translation (in vivo) |
Co-translational | Amino acid modified in translation (for example, myristyl glycine) |
Pre-translational | Amino acid modified before integration into a protein (for example, formyl methionine) |
Chemical derivative | Chemically induced modification (for example, during sample preparation) |
Artifact | Modification made during sample preparation |
N-linked glycosylation | Glycosylation (in vivo) |
O-linked glycosylation | Glycosylation (in vivo) |
Other glycosylation | Glycosylation (in vivo) |
Synthetic peptide protection group | Protection group used in chemical peptide synthesis (for example, the trityl (or triphenylmethyl) group) |
Isotopic label | Label for quantification |
Non-standard residue | Amino acid derivative (for example, selenomethionine) |
Multiple | More than one classification possible |
AA substitution | Amino acid replaced by another amino acid (mutation) |
Other | Modification not fitting into another category |
The application uses the classifications from unimod.org, the protein modifications online database for mass spectrometry applications. You can also manually define your own classifications.