Cross-linking

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Setting up a new cross-linking reagent

If you cross-link proteins using chemical cross-linkers or need to search for already cross-linked peptides, GPMAW offers a function that will list all potentially cross-linked peptides. The function is quite flexible, as you can define any 1 or 2 proteins and can define your own cross-linkers.

You start by opening the relevant protein sequence(s) on the desktop.
Then select Search | Protein MS X-link from the main menu.
In the “Select proteins for cross-linking” dialog you select (highlight) one protein as the A sequence and one for the B sequence. If you select the same protein on both sides, you test for internal cross-linking.
Selecting “OK” brings you to the “Cross-linker parameters” dialog:

In this dialog you first select cross-linker type.
Depending on the selection, the cross-linker drop-down box will fill with the appropriate linkers available in the local database.
If you cannot find your cross-linker here, click on the Setup button to edit the database.
The cross-link from to is set by the database.
Compositions are set by the database, but can be edited.

Finally you select the enzyme selected for cleavage of the protein(s), number of missed cleavage and the upper mass limit you want to analyze.
The enzyme you can select are from the standard list available in “Automatic digest”

Select “OK” to get the final list of cross-linked peptides.

Site last updated: September 14, 2017

The list will show the mass of the cross-linked peptides, where in the sequences the peptides originate and the type of linkage:
Peptide: non linked peptide
X-link: cross-linked peptides
Linker: peptide with hydrolyzed linker attached.
X-link + linker: Cross-linked peptides with an additional hydrolized linker.

The contents of the list is controlled through the buttons below the list.

You may compare the list to a peak list by selecting the “Compare to ms list” button.

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